All decks aren't created equal: some are Splinter Twin, others are Mono-Green Aura Stompy. The same goes for every set: some are Dominaria, others Legions. Thus, the impact of every new set will be felt unequally both by Modern as a whole and by individual decks. Not every set can have Modern-playable cards, and not every deck can get something new. When the new set is named Modern Horizons 2, the effect is far more profound. However, every writer and their hamster is currently gushing over which cards are busted and the decks that they allegedly bust. So I'm going to take a different approach and discuss the top decks that are hurt by MH2.
I should note at this point that "hurt" is a relative term. Every deck's relative power rises and falls over time. It's not fair to say that Heliod Company is harmed by MH2 just because it received no cards or because its position within the metagame worsened. The metagame raises and lowers decks all the time and power is always relative. Rather, I'm going to look at the decks that have new cards aimed directly at them. Hateful cards. Cards meant to disrupt or even completely defeat certain decks. But it's not all negative. All these decks have options for overcoming the hate and enduring, which I will also cover.
It's Over, Tron!
There's really no hiding it: MH2 was clearly designed to mark the end of Modern's Tron era. Brad "Jund Guy" Nelson worked on the set, so lots of Tron hate is hardly surprising. As always, though, there's more to it than just that.
Wizards printed three blunt-force anti-Tron cards and three more which interact favorably with Tron. And by blunt, I mean that Break the Ice, Obsidian Charmaw, and Void Mirror might as well have explicit rules text saying "use this against Tron." Void Mirror is the most obvious, as it counters any spell that was cast without any colored mana. Tron is a deck famous for casting colorless threats. You do the math. Mirror is also effective against all the suspend cards in MH2, almost as if Wizards was providing extra incentive for players to play the card. It is also quite potent against normal Tron's cousin, Eldrazi Tron, as if it wasn't obvious enough.
I Have the Hate Now
Break and Charmaw are similar in that both are intended to destroy Tron lands. Technically, Charmaw destroys any nonbasic land, which means it is likely a shoo-in for Ponza. However, the cost reduction of Charmaw is targeted at colorless lands, and again, what deck besides Tron uses lots of colorless lands? The fact that it can hit Tron turn three on the play cannot be an accident. Meanwhile, Break costs two specifically to prevent turn three Karn Liberated. Again, it specifically targets lands that make colorless mana. It also hits snow lands, but that hasn't been too relevant since Arcum's Astrolabe was banned. Though it is worth noting that snow-covered basics are not always strictly better than regular basics anymore.
Finally, there are Rishadan Dockhand, Tide Shaper, and Vindicate. Vindicate destroys any permanent, which means against Tron it will usually be Stone Rain. However, it also destroys Karn and Ugin, the Spirit Dragon. Vindicate isn't specifically targeting Tron, it's just very good there. The Merfolk both disrupt mana, Tron's whole deal, but aren't specifically targeted against Tron. Shaper in particular is very good since taking a turn off to Spreading Seas was often necessary but not desirable for Merfolk since Seas isn't a threat. Now they can do both! If you'd ask me, it's obvious that MH2 was meant to put some pressure on Tron.
Except It's Not Enough
Shame it's going to fail at that, then. I hate to burst any bubbles, but there is very little chance of Tron being uniquely hated out by anything in MH2. It might lose some popularity initially, but Tron will easily recover and continue to fun-police all over midrange and prison. Mainly because the dedicated hate is easier to avoid than it appears. Mirror doesn't counter colorless spells (which actually would be devastating), just spells that weren't cast with colored mana. Thus it's easily defeated so long as Tron has out a Chromatic Star or a forest. It wouldn't surprise me if Tron started running Yavimaya, Cradle of Growth for this very purpose, giving them a way to tap even their colorless lands for G and empty their hand of said Stars for multiple big-mana plays. Break the Ice is black and can be beaten with Veil of Summer. Overloading Break is a win, but at that point, Tron was unlikely to win anyway. And Charmaw is only good disruption on the play.
Ironically, it's the non-targeted hate that will be hardest for Tron. Merfolk has always had a good Tron matchup thanks to its clock and Seas, and now it has a Seas that is a clock. Dockhand is also annoying but far less effective. Vindicate is great because it is still effective once Tron has established Tron. In other words, the new cards really haven't changed the matchups very much. Which is to be expected: there's been plenty of Tron hate for years now and yet Tron keeps being Tron (remember Assassin's Trophy and Damping Sphere?). And it probably will until Wizards just outright bans the Tron lands.
All Thanks to You
However, that's not entirely the cards' fault. The answer lies in the mirror. How many players have seen all the new hate, will assume that Tron's going to be hated out and/or dropped, and will cut their Tron hate? Be honest, you've at least thought about it. That's the main reason that Tron continues to thrive in Modern: players don't respect it. The addition of new hate, especially beatable hate, won't change the reluctance of players to try and hate out Tron. Despite Break's potential to Consuming Sinkhole Tron, I doubt that it will see much play because there aren't snow decks anymore, so Break only hits Tron. Yes, it does hit any land that produces colorless mana, but lands that do that are few and far between outside Tron. The new hate won't see enough play to actually impact Tron as a result. Except for Merfolk.
Dredge Is Dead... Again
Not so unlike Tron, every time there's a shift in the metagame or a new piece of graveyard hate, Dredge is declared a dead deck. And for a while anyway, it is. MH2 perpetuates this cycle with the addition of more graveyard hate. Green got two cards that shuffle graveyards into libraries in Blessed Respite and Abnormal Endurance, which do hurt Dredge to an extent. Respite also having Aven Fogbringer attached could also be potent against Dredge's alpha strikes, making the card quite desirable in a race against the deck.
However, the card that most screams DIE DREDGE, DIE! is Sanctifier en-Vec. The only threat in typical Dredge that Sanctifier doesn't exile is Narcomoeba. And the only answer that Dredge might run is Blast Zone. There's also Dauthi Voidwalker, which reads like a maindeckable Leyline of the Void. The only problem is finding a deck that wants to pay double black for a 3/2.
However, the bigger problem for Dredge is splash damage. Wizards wanted to make Reanimator a thing in Modern, and they might have succeeded with Persist and Priest of Fell Rites. Dredge gets by thanks to players underestimating it and skimping on graveyard hate. Which in fairness has been a decent strategy for the past few months. With Uro out of the picture, there weren't many graveyard decks to worry about, so players cut their Leyline of the Voids and Rest in Peaces. The potential of Reanimator may get players to start running hate again, and Dredge will suffer as a result.
...But Will Rise Anew
However, Dredge shouldn't suffer too much. I've been over this countless times, but the best hate against Dredge removes the entire graveyard. Picking off one or two cards just isn't effective. However, that's exactly the sort of hate that players will gravitate towards against Reanimator. Surgical Extraction is quite good against a deck all-in on one card, which is why it sees so much play in Legacy where there are several forms of Reanimator. I suspect players will take a page out of Legacy's book and run Extractions or possibly Faerie Macabre, which will marginally affect Dredge but again, it's Dredge; so long as it has a graveyard, it's dangerous.
Even if Sanctifier and general hate remain prevalent, that won't be the end for Dredge. The deck could just keep going and hope to dodge the hate. Sanctifier is a relatively narrow card, after all. There are also options to move in the Millvine direction. That deck has a far better backup plan should the graveyard be shut off and features payoffs that aren't black or red. Both Dredge and Millvine can theoretically win by casting creatures, but hate doing so. However, rather than use them for the intended purpose of self-mill, Millvine can use its crabs and Glimpse the Unthinkable against their opponents. Don't count Dredge out.
Forget About Mill
On that note, what about the dedicated Mill decks? As with Dredge, they're hurt by the green shuffle cards, in many ways more than Dredge. Shuffling back your graveyard against Mill is the equivalent of gaining 20 life against Burn. I have doubts that either shuffle effect will see much play, but Mill will definitely be hit by some splash damage. Blossoming Calm is a powerful hate card against Burn, enough that I expect it to overtake Timely Reinforcements as the sideboard card of choice. Thanks to it granting hexproof without restriction, it's less powerful but more versatile than Veil of Summer, and therefore counters Mill's Glimpses, Hedron Crab triggers, and Archive Traps. Otherwise known as their most damaging spells.
More importantly, it looks to me like MH2 is going to keep Modern at too quick a pace for Mill to be viable. Mill's been decent a few times in the past year, times which coincided with either 4-C Omnath or Heliod Company being the top decks. The former was easy prey for Mill, as it was a slow deck that drew a lot of cards, making Mill's job easier. The latter was a slower deck that usually "won" by gaining infinite life, about which Mill could care less. More importantly than individual good matchups, those periods were relatively slow periods for Modern where aggro was suppressed. It's easier to get to 0 from 20 than 53, so aggro is perfectly capable of racing Mill, and it often isn't close. Despite control getting more toys, aggro is also getting cards. And Reanimator also potentially outspeeds Mill.
At Your Peril
However, don't get complacent. When Mill gets the right draw of Crabs and Orbs, it is shockingly powerful. That just doesn't happen all that often. Additionally, it is entirely possible that the boost to control outweighs the help the various aggro decks are getting with MH2. If that's the case, then there would be a net slowdown in Modern, which is exactly what Mill is looking for. At that point, the control decks will need to be wary, because they're exactly what Mill is looking to beat. It's also worth noting that thanks to Wizards mainly printing non-targeting mill cards recently (presumably to cut down on the more dangerous self-mill), it may be built to overcome Calm should the meta demand it.
A Change in the Winds
I'd also like to note that all combo decks that don't win via Thassa's Oracle will be hit by Blossoming Calm, Storm being the hardest hit: Gifts Ungiven targets opponents, so Calm both counters the Gifts and protects against Grapeshot for a turn. If Calm is adopted as widely as I think it should be, then Storm and similar decks will have to rebuild. MH2 has provided a number of options for Storm to move into green, though I have no idea if that's ideal. Is Caleb Scherer still around? Somebody ask him.
Let the Hate Flow
Modern Horizons 2 stands to help out many decks. MH2 also stands to hurt certain decks. However, that will only be the case if players take the new hate seriously and actually play it. For this reason, I think that Tron will come through relatively unscathed. However, this is still the early stages of brewing, and we'll all just have to wait and see.