None of these problems seem insurmountable ones, though. A little trimming here and there and we can have the sleek MHR Lite of our dreams.
Aside: I should also mention there are some small issues with the resolution mechanics that I'd like to change, but these are something I'll come back to another time. Once the basics are in place, that's all just polish. Let's concentrate on the character structure for now.
Removing the two-tier Power structure is simple enough, you simply condense all the Powers into a single set and allow players to choose two for their pool. In the case of "Power bloat" -- where you've got a number of traits all describing a single idea (i.e. that Captain America is a Super Soldier, Thor is an Asgardian, or Black Widow is an awesome secret agent) I think it would be easy enough to simply fold them into a single, broad trait. You could call them Super Soldier d10, Asgardian d10, and Secret Agent d10, respectively.
As for the FX, my main problem with them is that there are too many. What I'd like better is a concrete set of moves that are broadly applicable for characters "pushing" their powers -- Spend a PP, "bump" up a die type, as an example -- which can be described by the player in appropriate narrative terms. So Iron Man getting that bump might be re-routing power from his repulsors to boost his strength for a "Sunday punch", while Iron Fist might be focusing his chi into his fingertip for a nerve strike.
Limits I think could work much the same, with a single set of rules describing the benefits which can be gained by activating a Limit, and a single rule for how to overcome a Limit once it's been activated. Each character might have a short list of two or three items that Limit them, which can be activated narratively as appropriate by the GM or the player as the game unfolds.
The goal here is to keep the flavour pretty much as intended, but sleek down the character sheet as much as possible.
Specialties are a case that might need a re-think, or re-balancing where certain things appear on the character. The easiest thing to do here is to fold a bunch of Specialties into a broader heading (i.e. Shadowcat's heap of Specialties could be reduced to "Teenage Prodigy" and Reed Richards would be "Genius Inventor"). The problem is that we'd be running into a bit of overlap here with broad traits (i.e. Super Soldier d10) under Powers. You could emphasize that Specialties have to be knowledge-focused (elminating things like Covert Master and Combat Master, unless they are describing the theory and background and not the actual implementation), which would reduce a bit of the duplication, or come up with a catch-all rule for this -- the knowledge and physical parts of the same broad trait (i.e. Secret Agent d10) need to be balanced in some way. Maybe Black Widow can have Secret Agent d10 as a physical Power, but if she uses it on the same turn as a Specialty she has to "step it down" a rank or two as a penalty. Again, broad rules and less clutter on the sheet are always better, in my book.
Milestones could work in a similar way to Limits, as described above, with the player setting down a brief description of what problems they want to be important to them in the storyline / Event (much like a Trouble Aspect in Fate) and getting paid off in XP when they come up in play. Sometimes it's not a good idea to try to re-invent something that's worked for many years in the hobby, purely for novelty's sake. There are things about having structured experience and "unlockables" that are appealing, but I'm not sure they work for me.
Aside: Oh yeah! I totally forgot -- there are THREE stress tracks in this game. Do we really need these? I would argue that we don't, and that collapsing them into a single stress track would make fights faster.