I don't understand. The Super Meeple suggested doesn't really add anything. Either people want meeples already so they play to get them or they don't.
People might want Meeples, but they can get them from playing their favorite game(s). A Super Meeple, particularly if it awarded a gold bonus equal to all of the previous meeples of that rank (or even half of the total bonus for a rank).
Some examples:
White Meeples
single white meeple = 20 gold
there are 7 games, if all white meeples are earned, a person would earn 140 gold total for earning all of them. At the time they earned the last white meeple, they would get both the 20 gold from that one, Plus they would now earn a white Super Meeple and get another 140 gold. (or 70 gold for the Super Meeple if it was decided half the total was a better amount)
Yellow single Meeple = 30 gold
Yellow Super Meeple = either 210 gold, or 105 gold
Gold single Meeple = 40 gold
Gold Super Meeple = 280 gold or 140 gold
Green single Meeple = 50 gold
Green Super Meeple = 350 or 175 gold
...
Black single Meeple = 100 gold
Black Super Meeple = 700 gold or 350 gold.
Actually, anticipating the Black Super Meeples might be a good argument for only granting half to total for the lower colors. When entering the Blacks, things would begin to change. The first two Black Super Meeples (blank and 1 dot) would continue to earn only half the total. But now they would begin to graduate.
Two dot Black Super Meeple earns - 420 gold (60% of the total)
Three dot Black Super Meeple earns - 490 gold (70%)
Four dot Black Super Meeple = 560 gold (80%)
Five dot Black Super Meeple = 630 gold (90%)
Six dot Black Super Meeple = 700 gold (100%)
In any event, the large gold bonuses from the Super Meeples (compared to the amount earned for a single meeple) would probably encourage people to expand their focus beyond their favorite games, to include all of the games offered, because that is the only way they could earn Super Meeples.
Now having said all of that, I have to voice a completely opposite point of view when responding to the second part of your post.
Also, there's something I think you're missing. When people get all the meeples in a game now, there's no incentive to play it ever again. For example, I will probably never play Finito again after I get my final Meeple. I would think giving people an extra reason to play ALL games would be a good thing for the site. You disagree. Alright. No harm.
The only incentive to play (and the strongest incentive to play) is simply because the game is fun to play. The meta game(s) might actually interfere with this important reason that people play.
So an opposite point of view might be...
1. There should be no meta game, no meeples, no kings favors (except possibly for people who wanted to play the map game with the houses).
2. The site should not try to "encourage/control" people to play any particular game. Rather they should just watch to see which are the most popular. If a game were very unpopular, maybe they would get rid of it and introduce a new game.
BUT they would probably also have to get rid of the concept of food to play games unless you have a subscription, because the more expensive games might be played less simply because people don't want to spend that much food on a game. So the cost of the games might very well be influencing people's "choices" and giving a distorted idea of popularity.
So my answer to your
no incentive to play (a game) is...
Great! That's wonderful!
The only incentives to play, should be the enjoyment a person gets from playing a game, or possibly socializing in a game. The meta game we now have might actually destroy some of the sociability, because both people are trying to "progress" in the meta game and their opponent is an obstacle to that larger goal, rather than a potential new friend.