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So,hear me out on this, but we've come to the point in Pokemon where there's most likely going to be 700+ of these lil buggers (maybe closer to 800 if we get a ton of Megas) and it's pretty obvious that 700 is just a placeholder. We're going to get more Pokemon gens, more games, more Megas, and whatever else the future brings. At this point, nearly everything about Pokemon has evolved. The Pokedex, the Pokeballs, the battling scene, the exp system, EVs, IVs, etc. etc. It's all changed, and mostly for the better. Except one thing: the team size.
We still have six slots for 700/800+ dudes and its going to increase and increase until either Nintendo goes out of business or Pokemon suddenly stops generating tons and tonnes and loadsa dosh. There are two things I think that could evolve the team slot size while still keeping the fun of picking and choosing and mixing and maxxing.
One: There could be some kind of reserve system, like having a starting line and players on the bench. Some kind of quick delivery system where you put in, say, a dozen or twenty of pokemon. In the menu, there's an option for a quick switch, where you can bring in pokes from the reserve list you set up at the Pokemon Center like you're working a PC. Lot quicker and more fluid than having to pick which pokemon you're gonna dump and which one you're gonna replace.
Idea Two is much simpler: Give us more space on teams. 8, 10,12, who cares, just give us more. This would make the game more difficult, as you might face trainers with upwards of 8( or 10 or 12) Pokemon at once. Maybe even implement it as a choice at the start of the game, like Challenge mode in BW2. Just pick your team size, and the game scales accordingly, even if its as paltry as adding a pokemon or two to a gym leader or trainer.
Anyway, just a thought. Have at it.