He can work in a 2 man midfield with a proper defensive midfield partner, but when you think about it, all the best teams have 3 man midfields. Would Iniesta work in a 2 man midfield? Would Thiago? In a 4-2-3-1, he played at his best for the national team as one of the deeper players alongside Besic, and not only against the usual mediocre opposition, but against good teams too, so it's not like . I wouldn't worry about the Mata situation, as Pjanic is an actual central midfielder and not a #10, and he does work relatively hard defensively it's just he's play maker (either advanced or a deeper lying one) so he's obviously not great defensively and that's not what you have him in there for.
On the other hand, I don't think he would particularly suit Mourinho, would've been perfect for Van Gaal though. Though then again, play style he's very similar to Fabregas who did play really well initially for Mou, only I'd say Pjanic is a bit better technically (like his dribbling and being more agile on his feet). Also I'm not sure how he would do in the premier league, as before he was relatively injury prone (not that much anymore), and he is used to a lot more time on the ball and a slower pace in the Serie A. Big part of the reason of why he plays so well there consistently. Think he's just more suited to Serie A or the Spain, instead of England/Germany. Might be one of those players who would struggle to adjust to the pace and power of the prem, but if he did, then there's no reason as to why he wouldn't be brilliant here.