You still need to wisely use your X-Factor, be it a guard cancel or what have you. A lot of players know now in what situations you can get your shit pushed in by X-Factor and you can actively avoid them or bait them. I don't understand what you mean by "guaranteed" damage at all, nothing is guaranteed so long as both people have their hands on their controllers. Also, X-Factor is still balanced by player skill too, opponent can always counter-XF, and at the end of the day it isn't like if there's a lone person in XF they're invincible or anything. I don't know where the assumption comes from where player skill is thrown out the door with X-Factor. If your better, in the context of the entire game and in that instance of being up against someone with the X-Factor advantage, you can still prevail. When you activate X-Factor it doesn't turn into a single-player QTE or something.
Marvel is just a riskier, more volatile game so X-Factor can generally get you further, there's a lot more dumb shit and option-selects you can get hit by, so the effects of X-Factor being something that is active for a duration of time rather than an instance is much more noticeable. But, fundamentally, they work very similar as comeback mechanics, and I can't vouch for any game needing them. I would love for SFV to return to just a super bar. Ultras feel extraneous, and unnecessary, like all comeback mechanics really.