Fair points, but I think your missing one key factor. One of those players played in a side that absolutely hammered the league (for the first half anyway. Then went a bit defensive which would play into his style), the other was in a recently promoted side and has gone through the divisions, while every year upping his game.
PFA team of the year doesnt really count for anything IMO. The big sides are always more likely to contain players than the lower sides. If Matic and Schneiderlin are similar, Matic will 9/10 get the nod (even though IMO it should be the player thats playing just as good in a 'smaller' team).
Again, Chelsea having the best defence by 10 goals. ITS CHELSEA lol. Champions. Arguably have the best GK, Right/Left and Centre backs in the league (Cech/Courtois, Ivanovic, Terry, Azpilicueta).
Also for this season you could argue that if Matic was anywhere near as effective as what he was last season, Chelsea could and probably would have a few more points than they have now.
Taking into acount the teams they play/ed for, and how each player has carried on their form over a few seasons, I'd give it to Schneiderlin. At one point you could maybe argue Schneiderlin appeared better because of Wanyama, but hes gone onto United and pretty much finished where he left Southampton. Even if the team itself has been pretty inconsistent.