The problem with sidlining them without it being something major is given theirs and our profession is saving the world(s) theres no reason for them to stay sidelined in that instance, if the world is ending or threatening to end then Thancred is getting out of that bed, Y'shtola is cutting her vacation short.
Even when you give them important goals of their own, like how Lyse is helping rebuild a nation, what good is that if there's no longer a world for that nation to inhabit? She was sidelined by force, she'd have come if she could, but physically couldn't.
Now you could do it and they have in the past by simply giving them equally important plot things to do, like how Thancred was absent for several patches while he crept about in the Empire.
Personally though, I'd rather they didn't, I really like having them with us, most FF's you have your main party throughout and while some members come and go you often have your core team for the majority and I like that.

As for what I'd like to see, outside of the obvious ones, I'd really like to see a new healer, I'd like to see either something done with the companion system, they teased us back in 2.x with our Magitek armour being one, but the system has been long abandoned, I had hoped perhaps that was the end point for the Role Quest NPC's, they'd be travel and combat companions, and with their intergration into the MSQ my hope remains.