"You've witnessed changes to the story and mythology that clearly were never in the minds of the show's creators when it all started"
This isn't necessarily a problem either, at least not in every single case, but I will say that in this 5th season that I can see the gears cranking in the writers' heads a lot more clearly than I used to be able to. Really this problem arises most when it's obviously time for them to kill somebody off, which is admittedly a problem that plagues a lot of other shows as well. And yes, the time travel thing is pretty transparent.
All in all though, I was prepared for this--ANY show with a "mythology" or a big mystery will typically be more interesting before they have to come up with answers, than when they have to. This was a problem with The X-Files, obviously, and I was prepared for it then, too.