Eeeuuughh...
The entirety of a topic like this would better be discussed in Pokemon general, I feel. I don't want to drag it down, in that all the OP wants to see is a Safari Zone in X/Y without limits, so more of a speculation request. And that would be neat I guess.
But thinking about zoos overall for Pokemon? Uh, that's...
If you are one to think that Pokemon belong in zoos, you are not giving them nearly enough credit. I guess as humans, we only see other humans as being capable of sapient thought, but Pokemon have proven themselves to be this way as well, and that's were things start getting extremely grey. I wouldn't put another human being on display in a zoo like setting, and when people do, they usually call those freak shows. Pokemon aren't robots, either. And yet, there's no doubt that they seem to be fine traveling in a Pokeball, but I guess that's out of a mutual understanding?
The Safari Zone works well enough, because in terms of scale, the Safari Zone would be massive. The boundaries are spread so far apart, that I seriously doubt the Pokemon would have any issue living in that area. The isn't a whole lot there that would make the creature feel trapped, and honestly, they probably wouldn't venture off miles beyond the spot where they made their home. It would be similar to living in a gated community.
Anyway, I'm not trying to get too deep in this, at least here. I just saw the word "zoo" and alarms went off in my head or something, haha.