On that note, while I usually get on the Clone Saga band-wagon for hateration, there's one bit of an ironic point that I just can't ignore.
For better or worse, the Clone Saga's ORIGINAL ending would have served for Petey (the clone) to lose his powers, retire to some place in Montana and live happily ever after with MJ and the Spidey-baby. Ben, meanwhile, would have served as a means to take Spiderman back to a character who was a bachelor, and endure everything that comes from single-life and super hero, as well as the tragedy of a guy who lost out a good few decades' worth of the life he was meant to have. Apparently, THAT wasn't good enough, as the combined bitching of the fanbase wanted and brought PETER back.
So, in the end, we lose a perfectly good guy like Ben, just for Peter to have, among other things, a "failed pregnancy", MJ and Petey to have a marriage on the rocks, Peter to get the revelation that Gwen was [tornado fang]ing NORMAN OSBORN ON THE DL (and had two freaky kids as a result), reveal his secret identity to the world and then make a [tornado fang]ing DEAL WITH THE DEVIL HIMSELF....all for Peter to go back to being a single-guy who lives with Aunt May, all over again.
Was the trip really necessary, if all that was going to happen is some thing akin to the result that yielded from the Clone Saga's original ending, any way? This is why I really loathe Marvel comics right now. It's fundamentally as bad as what they did with Cyclops back in the day. They may have retconned it several times, but that's just to try and make Scottie's act of abandoning his WIFE AND CHILD to pursue his dead girlfriend look better! 
Oh, I'll be the first one to say that as terrible as I think the Clone Saga is, I think the Spidey-Mephisto OMD thing was the worst event in comics history. It was just the climax of about 5-6 years of god awful Spidey writing, and all it showed was that "With Great Power comes ZERO Responsibility." It's essentially the Midichlorians of Comic Books. Almost everyone says that after OMD, Spidey has gotten better. WELL, IT COULDN'T POSSIBLY BE MUCH WORSE........unless Loeb took a crack at the Web Slinger.....
Yeah, some of those plots had potential, but they overdid it a bit.
Hell, the title of that was "I Really Really Hate Clones!"
To be fair, as much as I am not a tremendous fan of the 90's Spidey show, I will admit that The Alien Costume 3-parter to end Season 1 was actually very well done and very well written. After that though, save for a few episodes, it just never really impressed me all that much. 90's X-Men I thought was great until after the 4 parter with the Axis of Time.
As for final boss on the Marvel level, Annihillus would be one of my picks. Galactus would be pretty odd, but fun I think too.