I LOVE having my pokemon out in SS--it's epic. Also, I love the extra story you sorta get.
As far as it goes though, the thing I least like is linearity--I like choice in what I do.
I also dislike having to teach Flash in a lot of cases, because it usually means I have to carry around a useless pokemon for a while. WHY CAN'T MY AMPHAROS JUST LIGHT UP ITS TAIL?? Heck, it's the lighthouse/beacon pokemon, for crying out loud! It shouldn't need an extra move to do what it naturally does.
Trading to get pokemon is also an issue with few people I know having the same generation games and an iffy Wi-Fi connection.