There was some good and bad brought on by those two last seasons.
The addition of Robert Patrick and Annabeth Gish were very good ideas, so was the Mulder abduction storyline to cover for the partial loss of DD.
However, there were a few problems: the way 1013 handled and resolved the Mulder storyline, the way they wrote Monica Reyes' character, the MOTW that were just too 'out there' and two-dimensional to be memorable and scary, Scully crying too much, the Super Soldiers
, killing Krycek, killing TLG, putting William for adoption, etc.
Yep, I'll get back to you when I finish watching the series.