I used to hate that sort of thing - when the game makes unexpected decisions for you/splits up your party or forces you to use certain members without your sayso. Ever since Summoner tho, I don't mind anymore. It really just depends on how it's done.
Didn't console games tend to do this a bit more often than PC games, at least in the past? I seem to remember reading reviews that mentioned that, ages ago. If so, then since consoles are starting to take over somewhat, it's not surprising to me that it's starting to occur with seeming more frequency in PC titles.