In spite of the spectacular ways in which JJ Abrams has jumped the shark with Alias, it is nothing when compared to the convoluted mess that was XF canon by the time Season 9 concluded. I think (without, obviously, presuming to actually know *g*) that this might be part of the reason that you have trouble with XF and not Alias. Alias is easier because the knots are simpler to unravel; XF is harder because once you decide to ignore canon for a story, you have to decide just how far you're willing to go.

That's not to say that Alias won't eventually plumb the same depths XF did WRT incomprehensible canon, but they haven't gotten there yet. *g* (Though I should note that I've stopped watching Alias, and am mostly satisfied with my decision to do so.)