1.) You could classify all the different spots on each map into different categories, so the sample size wouldn't be as small. If I play field of the great phoenix on the left spot, my rating could be based on "Choke-point big team maps-land spot" or the like.
2.) Expanding on that idea, theoretically, you could alleviate this by having a dynamic rating that, in a given lobby, weights most heavily towards games on that map in that spot, weights second most heavily towards games on that map in a different spot or games in a similar spot category (choke point big team land spot etc.), and finally weighs least heavily towards all other games.
So, on twin rivers air, my rating would be weighted most heavily towards games I've played on twin rivers in the air spot, where I win a ton (say I'm 1700 in that), then towards twin rivers (maybe I'm 1500) and 10x10 team maps where I play air (maybe 1300), then all other games (maybe I'm 1200). So, my rating in that spot would be 1500. But, if I switch to a land spot, it would probably drop to 1300 or 1400. If I join a seton's game, it'll be 1200 in navy, 1000 in air, and 900 in ground etc. because I don't play 20x20 maps as much nor have as much success.
Anyways, like I said above, I think this would all be a bit too complicated and probably hard to do, so I'm not advocating for it, but it's just what I saw as a way to implement the idea.