Iron Man 3 was the most underwhelming sequel/follow up I've ever seen in my life. Iron Man 3 is The Phantom Menace of the MCU. The guy faced off against gods and aliens in the last movie only to be followed up by a ******** ex-fanboy. You'd think after 2 corporate non-threatening villains and after finally proving his worth as a real superhero when the time finally came you'd think he'd be facing bigger stuff like the real Mandarin.

You can't be serious. So monopolizing a global conflict, all while having a reproducible super soldier formula isn't threatening? If anything, Killian came as close, if not closer, to world domination as Loki did, not to mention that he stripped Tony down far more than any of his previous adversaries had.
As for your other point, I have to wonder if you feel that way about other franchises. Lex Luthor, another boring corporate villain, as you put it, will inevitably make an appearance in Man of Steel's continuity. What's your take on that? Thor didn't just save the known universe, but
existence as well, and he'll be taking on an A.I. in the next Avengers film. What then? Let's not forget that Supes saved the planet from a platoon of gods himself. Going bigger isn't necessarily better; get some perspective.
I get that you dislike the movie, but at least be reasonable about your criticisms...and consistent. IM3 had its issues, but the stakes not being high enough most certainly weren't one of them.
The most entertaining aspect of a superhero film is the overcoming of obstacles like defeating the bad guy.
That's an oversimplification. If it were in any way true, then Transformers would be the benchmark for all action/superhero films. You can't nail down a genre movie to such a simplistic concept; there are far too many variables that contribute to entertainment as well, and movies are, as well as any other fiction-based medium, about the sum of all their parts rather than just the individual pieces.
Even if they decided to go with that silly twist, the least they could have done was develop Aldrich Killian's character into a legitimate villain who gets finished off by the titular character. Shane Black committed a cardinal sin here with what he did here and what he planned to do and I hope to god he never touches a comic book movie.
Again, I don't see how you can say something like that. Killian's plans and end-state were one of the more original ideas in the genre as of late, and while I agree that he could have used some more development and originality with regard to his character, he was far from being the irrelevant villain that you seem to be suggesting. What cardinal sin are you even referring to? There's too much inaccuracy, generalization, vagueness, and hyperbole in your assessment for it to be taken very seriously.