Two of the issues I have are with the way the Powers are handled. Each character in MHR (well, most of them) has two power "sets", and the standard way of using powers in your dice pool is to choose one power from each set. This is fine as a general orientation in the game, but doesn't work quite so elegantly in practice. Sometimes the distinction between the power sets seems arbitrary, and characters who have a smaller number of powers feel like they're a little shoehorned into this structure. Secondly, there are a number of characters who have a wide variety of middling Powers that refer to above-average physical and mental traits. Okay, Captain America is strong, agile, and tough -- but do we really need three Powers to describe that?
Also, Powers come with additional bells and whistles called FX and Limits. These are "baked in" ways to push your powers in ways that are appropriate to the character, generating bonuses in specific circumstances, or (in the case of Limits) creating situations where your Powers fail or get stepped back temporarily. Limits help you generate Plot Points, which can be spent for all kinds of fun effects in the game. I like the idea of all this, except that there are way, way too many of them on the characters -- the sheet just gets cluttered with piles of tiny writing explaining how each FX and Limit works.
Too much of a good thing is also the situation with Specialties, the system's way of handling skills. Characters like Mr. Fantastic or Shadowcat, who are supposed to be super-intelligent, or Black Widow and Hawkeye (who are superb, but not superhuman, physical specimens) end up with piles of skills to show their awesomeness. Isn't there an easier way to "beef up" the super-normals without putting all that system bloat there on the page?
Finally, we come to Milestones, the system's newfangled take on Experience Points. Each character has two Milestone "themes", which are appropriate to the character; when these themes come up in play, the character earns XP. XP can be spent on upgrades to the character, including new FX, and also story-centric upgrades (such as unlocking the ability to be an Agent of SHIELD for the story in progress, or gaining access to a particular character or piece of gear). Each "theme" has three "triggers", one (1 XP) that should be able to be triggered at least once per scene, one (3 XP) that should be triggerable once per session, and one (10 XP) that's once per storyline and represents a big change in the character.
For example, Cyclops has the "Romantic Tragedy" Milestones path. He gains 1 XP when he chooses to express his affection for another mutant hero; 3 XP when he turns down aid in order to be alone with his chosen paramour in a dangerous situation; and 10 XP when he either watches his paramour take d10 or more trauma or breaks off their relationship in order to save them.
Milestones are intended to be very structured, working as part of the "Event" scaffolding that the game sets up for adventures. This is sort of an interesting notion, because it supports the idea that in a big Event storyline you're going to play in more of an Ensemble style, with each player perhaps taking the parts of various Marvel good guys during separate parts of the story. That's cool, and gives you a nice way of building the expansiveness of the setting into the game. I'm not sure it's exactly a good idea that XP unlocks various upgrades for the characters, in the style of a video game; sometimes it's just not going to make sense that the player characters become agents of SHIELD, I think, and if you really want The Sentry to show up in an adventure then it shouldn't be a story "switch" that's on or off, that should be important enough to be part of play. Making that character only available if enough XP are paid means that any previous encounters with The Sentry may be moot. His presence in the story is mechanical, not causative.
The bigger problem with Milestones, apart from weird in-story effects being created by XP "purchases", is the fact that the example Milestones are sometimes geared toward roleplaying that is broad to the point of low comedy. Yes, it is an important part of Iron Man's character that he is an alcoholic, but setting up alcoholism as an in-story Milestone which pays off in XP for unlikely and irresponsible behaviour from Iron Man (showing up drunk to a fight, passing out) is not a recipe for satisfying roleplaying. And indeed, in an Actual Play podcast I listened to of the Breakout event (included in the rulebook), a player simply declared that Iron Man was doing those things to cash in and get an XP reward. This is the other problem with Milestones -- they are ripe for abuse.
So, how do we sleek down some of the bloated parts of this character structure and get Milestones to work a little better? Stay tuned, True Believers!