Firstly the lack of Iron Man in the film. That is always going to happen. It happens with Spiderman as well. To tell the story he can't be in the majority of the scences. If he or in the case of these films Iron man were it would just be 90-120 minutes of fight scenes.
One of the things that messed up Spiderman 3 so much was bringing in Sandman and Venom in the same film. You have two origin/stories to tell.
Secondly about future films being Iron man fighting "metal men" that I feel is basically all they will be. Firstly they have yet to use Crimson Dynamo and Titanium man, both of whom are more guys in metal suits visually.
Secondly and more importantly. Iron Man is limited bgy the fact he isn't as well known to non fans as say Spidey, Fantastic Four, Batman etc.
I'm not an Iron Man fan so my comic book knowledge of him is serverely limited. The main villain people on IMDB seem to want is The Mandarin. I know of him and that he is one of the, if not the biggest adversary of iron man, but to non readers of the comics he is "The .....Who??
In comics you can get away with a lot you can't on screen as you are telling a fight in maybe 20 frames. So even someone that is a bit crap can look a bit dangerous. When they appear on screen they are likely to look crap. Whiplash came over like that in this film. Had he been fighting Spidey, Daredevil, Black panther, basically a guy with jusst latex to protect him it would have worked better. For this reason I think Iron man is going to keep going with him fighting more "metal men" aircrafts etc.
If they do want to avoid that I can't see where they can go with Iron Man as he is too powerful and too technicalogical a character.
Mandarin - Wont work as a serious threat on screen
Absorbing Man - possibly
Unicorn - Crap and neeRAB to be avoided.
Lastly you said about there being so much of a yawnfest in the middle. There is a rumour (isn't there always) that the next film is going to deal with Stark's descent into alcholism.
If they do go down that route there will be even less Iron man as it will become a drama piece rather than an action film. Doing a descent into that kind of problem over many issues lasting a year maybe more is one thing. To try and carm it into a film lasting two hours is another.
IMO they should do the third one (if they really must) they are planning on doing, do The Avengers film and then ditch the franchise. Iron Man doesn't work as a film character.