Will the second playable character only be used at certain plot points in the game?
I imagine this is exactly how it is going to work. Pretty much used in exactly the same way as it was in TW2.
The assumption, and hope, is that they will have learned from TW2 and make it so that when you take control of another character, it feels good and if the character has new skills/abilities, or more importantly can't do certain skills Geralt can, then you will be notified as to not make controlling that character a pain in the ass.
Honestly I loved the sequences in TW2 where you got to control another character in regards to the storytelling and character building, the only issue was the aforementioned control problems. The characters had an extremely basic "soldier" move-set, which made them feel very clunky, and not being able to evade made the scenarios problematic in that sense.
So whether or not the playable character in TW3 will be a "nuisance to play" will entirely depend on how it's implemented, and hopefully they'll have learnt from TW2 and improve it. As for the Story, I don't see it being a big issue at all, as I said I felt moments were enhanced in TW2 by being able to play as those other characters, and presumably it'll be used to even greater effect in TW3.