I just don't see Scully as a "bad" character at all, if your watching the X-files mostly for a hard sci fi story arc which makes a lot of sense then honestly your watching the wrong show.
The main appeal of that show was always the two leads, two great well rounded characters with loads of personality who could be put into endless different situations. You have to suspend disbelief even on a basic level of just how much stuff happens to them(they should be PTSD ridden physical wrecks the amount of times they've nearly been killed by various monsters) but if your able to do that I think theres a hell of a lot of very fun stand alone episodes.
Again I think thats something which is missing from a lot of modern sci fi shows, stuff like the X-files, TNG, Quantum Leap, etc were you had well written self contained stories over 45 mins which could cover a lot of ground in tone/style. Now its basically all long serial stories which are mostly deadly serious but IMHO often actually more juvenile.