People like fun things, which should be reason enough for them to include it.
Limitations would definitely need to be set. A switching cool-down or even limiting the number of switches per battle would be one method of keeping fights form becoming stall-sessions.
Even with the simplified mechanics of Go, raids are much easier to optimize for over PvP battles. You know what the target is, you know how much you need to power up your squad, you know what specific set of moves to give your team to fight it - at most, you need to watch out for a specific moveset.
PvP has different variables in play. Did you know, for example, raid bosses have lower base stats than normal, barring the obvious HP? In PvP you're fighting against opponents at full strength. You thought Blizzard Kyogre hurt now? Better brace your ass when there's an extra 65 base points of attack behind it. On that topic, it invites people to play with different moves to wreck more optimal counters. Maybe there will be a prestige-like system, where the bigger the CP discrepancy between you and your opponent the better the rewards should you come out on top.
I think that (read: hope that) PvP will shake up the combat system. I think either way people will still do it. People had similar critical outlooks about trading, saying it "served no purpose" yet with introductions of things like bonus candies and lucky chances they've found a way to keep people involved with it. While I don't know what exactly they'd do, they'll likely do something similar to keep people battling.