See, that's one problem I've always had.
Those are some very generic ideas, mate. The whole making a 386+ patch is just illogical. It'd be to the point that you don't encounter the same Pokemon twice. The most Pokemon you should have in a game, in my opinion, is roughly 210. 150-170 in the regional dex, and the other 40 or so available as post game.
I also don't like the idea of all the legendaries. I know you only said five of 'em, but still, encountering a legendary should be an extremely special thing, so I think two is more than enough.