With Dr. Strange, The Inhumans, Spider-Man, The Fantastic Four and more coming up, there are a boatload of villains that would be great side characters or leads that have yet to be used.
Ultimate Norman Osborn:
You're probably thinking that we have seen him already. No we have not. This Norman Osborn has always been a jerk. At least with the Norman in the 616 Universe we could say that he may have been an absent father but he cared about his son until he took the OZ formula. This Norman didn't give a flying fig about his wife or his kid ever. For this Norman Osborn it was all about power. Whether it be by acquiring wealth, businesses, or superpowers. At first, Norman was trying to recreate the Super Soldier Serum that made Steve Rogers Captain America and accidentally created Spider-Man. He then experimented on himself and became the Green Goblin. So not only do we get the Green Goblin, we also get selfish and obsessive Norman Osborn that has hired hitmen to kill a person he knew was just a teenage kid. He is a horrible, despicable, and disgusting human being and that is everything we want in a villain.
Norman Osborn has to be a jerk. This version was an @$$-hole right from the beginning. Other than being a genius Norman has no redeeming qualities. Keep it like that.
The Lord of Chaos Dormammu is one of the many demonic forces that have tried time and time again to make their way into the mortal realm. Whether it be Dr. Strange or Thor, Dormammu's plans have been thwarted time and time again. The great thing about Dormammu is that he can be used as a villain for Thor VIllain as well as a Dr. Strange. The cartoon movie showed him more as a being of pure energy and in the comics he has a form that appears to be armor holding in his energy form. Either way, what Marvel can do with him on the screen will be nothing short of brilliant. Also, if you get Dormammu you could eventually get the next character.
He has to have a flaming head. This isn't even up for debate.
Parker Robbins is the poster child for overachieving. First he accidentally falls into some powers and makes some cash doing so. Then he gets a bunch of villains to work together to make more money than they've ever had and avoid doing jail time. After he lost his powers, not once but twice, Robbins still didn't give up. He tried again and again and was almost the first mortal to have possession of the Infinity Gems. Parker Robbins refuses to just be a normal guy. But who would after getting a taste of real power?
Parker Robbins has to be street savvy and have a bit of a swagger to him. It's one of the personality traits that makes him so great.
Paste Pot Pete a.k.a. The Trapster:
Paste Pot Pete is a joke. Let's get that out of the way now. But here is the funny part, he is actually a genius. He doesn't just have the paste that he created. He also has a few other mechanical inventions that he has used against the Fantastic Four (when Storm and T'Challa replaced Reed and Sue Richards). Even T'Challa was impressed by Trapster's inventions. The problem with the Trapster is that he spends more time using his glue guns than his other inventions. No one is going to take a guy serious who who shoots glue at people. Sure, he's beaten Deadpool, Iron Man, The Thing, and Johnny Storm. But all we see is a guy who shoots glue at people. Trapster may not make a great lead villain, but watching him get the crap kicked out of him while people are making fun of him would be worth a few laughs.
As much as it would be cool to see him be all he can be, it would be even funnier to play a loser. Maybe get one win and then lose it being an idiot, but he should probably be a loser.
Kl'rt The Super Skrull:
How KL'RT hasn't been used in any of the movies perplexes me. And no, when Johnny Storm borrowed the powers of all of his teammates in "Rise of the Silver Surfer" does not count. That being said, didn't it look beyond cool? For that reason alone, Kl'rt would be a great choice. Besides that, Kl'rt is a powerful warrior without the powers and a general in the field with his soldiers. Kl'rt isn't a funny character, but he is very brutal and has always used his powers very creatively.
Kl'rt has to be confident. That is the biggest part of his character. It may come off as arrogant, but it is completely justified. No matter what happens to him he will continue to fight. He could be alone fighting The Fantastic Four or an entire army with no chance of winning and Kl'rt will keep on fighting and he will do it while talking trash and even sacrifice himself to win. All for the glory of The Skrull Empire.
Ultimate Mole Man is one of the strangest villains in the Marvel Universe and his Moloid creations are just as strange. Mole Man is a creepy old man who hides in the bowels of the earth and creates mole creatures and monsters and calls them his children. Mole Man would make a creepy and disturbing villain. In the Ultimate Universe, Mole Man used to work in the Baxter Building as a teacher and was fired for continuing experiments that he was instructed to stop. Maybe he could creep into the bedrooms of people in the Baxter Building and look at them as his children because he went completely insane after being fired. Either way, he'd make a eerie villain.
He has to have creative looking moloids. Since Mole Man doesn't fight and lets his "children" fight for him, they will get most of the screen time. So they have to look original and weird.
Thank you for reading. If you have anything to add you can leave it in the comment section.