Hmmm...I can see what you're saying. Only pokemon I know of so far that is for sure restricted is new, which is pokeball plus only for now. I imagine zapdos and the other will be available though considering me mewtwo is another big part of the game and already confirmed to be in it. As for missing raids, the legendary birds are being cycled through as a "research reward." Read on serebii that zapdos was cycled out for articuno recently, but I could see it coming back. Looks like it doesn't take too much work either to get the research rewards. Plus I don't think microtransactions will be a thing because arcticles are saying that you can get various pokeballs for just beating trainers. Like I said though, I can see what you're saying. Too much GO influence isn't going to be good. It doesn't encourage hardcore players to play with newer players like Masuda wants when the game is too much for the casual/newer audience.
The thing is I also dont live in an area where I can complete these goals.I tried once and I have to go out of my way to do any of it. The main issue people have right now is we have to play GO again, and we dont want to. That is all I'm worried about to be honest but I don't see why this couldn't be on the 3DS.