I don't know how it currently works but that section of the homepage is populated by MMOs and idle games with save function. This means games that get someone to come back and play it over and over seem to have a bias to getting to the front. Whether someone comes back to check a game every day or plays it once, it should count the same towards the " popularity " of the game. Smaller games have no chance of getting up there even if they are really good the way it is now.
This is so weird, I was literally just looking at the Popular Games sidebar and wondering what the criteria was...
For example, Goodgame empire is only rated 63 with 250 something K plays, meanwhile there are other games on the front page and off the front page (like Aground) that are blowing it away in ratings and plays.. It doesn't seem to make any sense.
Last time I checked, the admins decide what games go in the ''popular games" section, which means the solution is to either rename that section or come up with defined criteria and redo the section based on that. Such criteria could include the number of players, which is not currently visible to users (plays is the total number of times a game page has been visited).