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It's half as big as the moveset data, and not much compared to pictures. However, it's still big. I did think of a way to trim it down some more though; I think I can get to a quarter meg.
Pictures can be streamed, and moveset data is a huge problem for PS; it's already our largest data source and responsible for a noticeable proportion of the size. And you've said that OU is only one metagame...
Any given OU through NU stack should merge without too much harm. I'm iffy on Ubers, LC would be very shaky, and cross-gen stuff even shakier still. I would highly recommend only enabling the feature one tier at a time though.
Ubers should work the same way as OU-NU. There are rarely LC Pokémon usable in other tiers, so that shouldn't be a big deal either. I'd probably just turn off the feature for past gens.
Bigger problem would be Hackmons, in which the feature should probably also be turned off. In most other tiers, though, generally if a Pokémon counters another, they're counters as long as both Pokémon are legal in the tier.
The only issue with Ubers is that better counters should exist, in which case we just weigh an Ubers counter higher than an OU counter, same as we go down the list.
Hm, is it a matter of which sets are more common? Oh well, rate the OU counter data higher, then. Incidentally, I don't know how you're storing the data, but I think just lists of the top 10 counters, sorted, for each pokemon, would be comparatively lightweight.
Yeah, I mentioned earlier that it can be trimmed down. I was storing the weighted version separately. And I later realized that I have the team co-occurance data in there too. So 1/3 as big as I said.