The good folks at MTGGoldfish have once again released some great data by analyzing MTGO replays. From watching thousands of Modern matches, they've made a helpful chart showing the matchups between the ten most popular decks in Modern. You can find a write-up from their findings here.
The first instinct of a newer player would be to say that the winningest deck, Bant Company, is the best deck per this evidence. Given the high diversity of Modern, this is a dramatic under-utilization of these data. The real value here comes from the matchup percentages. As SaffronOlive cites in his write-up, the Grixis control versus Affinity matchup reports in stark contrast to what many might believe. It has been said that Kolaghan's Command was a death knell for Affinity, but the deck continues to see success and even boasts a near-60% win-rate against Grixis control.
Taking a look at where a particular deck struggles will help you identify what matchups you should spend more time on and trying to make adjustments for. For example, Infect is a scant 32% against Grixis Control. This means that as an Infect player, you don't really have a margin for error in your play. Being aware of and avoiding any common mistakes will be crucial in this matchup, and developing sideboard technology will help you salvage a poor matchup against a relatively popular deck.
Another interesting piece of data is that players on the play win more than 7% more of the games. This isn't a surprising notion by any means, but it's good to have a more exact idea of the relevance of play-draw. It's unlikely that many people are thinking about drawing first in Modern, but it might be worth playing for position in something like a PPTQ to have the play in Top 8 knowing the extent that the play will help you.