Regarding Matos - I think Ferreira's preferred formation has basically resulted in him being left farther back than he played under Lucescu, on purpose. Basically as a third CB who could function as a pivot. I would have thought that he and Giannoulis would rotate more as far as who plays farther up goes, but either Ferreira is very reliant on Matos' superior defending ability, or he just wants him to get less tired during games.
The thing about our midfield is that we have a few decent players and then a lot of averageness. We need an Oliveira-type in there. Esiti doesn't have any ability to pass or attack (can this be fixed? hopefully!), which limits his usefulness. Augusto is, as you say, just average. Misic is the only one who really kicks ass out there (and hoo boy does he kick ass).
Akpom and Swiderski are very different players from each other. I like them both. Hell, I'd like to see them both play together more often.
Pelkas and Biseswar, btw, are both being played out of position in this formation. Biseswar has to play farther back in order to cover our underperforming midfield (and can't physically get up front fast enough to attack)....while Pelkas *can* cover the midfield by running, but ends up being physically exhausted and mentally out of sorts when it happens as often as it does. I think if the midfield starts to really click, that he'll be much better. We really shouldn't be relying on our attacking midfielders to play both DM and ST...