I don't think that it is fitness so much as the formation that we've chosen to adopt. By playing with 2 wingers we are leaving big gaps in the centre of the park. The midfielders have so much to do to try to plug the gaps that it isn't surprising if they tire.
It is noticeable how easy we are to play through even with 11 v 10.
Maybe if we are more compact, plug the centre more, have our midfielders closer together we can start controlling games more and tiredness and fatigue should be less of an issue.
the formation rather than fitness levels is what i think has cost us so far.