I think the problem that fans have has nothing to do with the storyline but with the characters solving it.
If you look at the storylines, the cases, itself you know they are great and that Chris Carter didn't lose his touch. I think we just see them different because they are investigated in a different way, with a different aproach. We are used to Mulder and Scully solving, or at least investigating, the cases in their own special way and in this season we lose that and we get 2 new characters, Goggett and Reyes, who investigate the cases in a complete different way. We loved Mulder and Scully's way so for us it's hard to see it different.
But I repeat, the storylines are still great, they are as x-files as they have ever been.