Freedom Force "suffers" of that. While your characters can do amazing feats, they are mostly balanced and severely underpowered in gameplay compared to what they can do in the story or to what typical comic supes can do.
Best example is the Alchemiss, one of the main characters. In the sequel she finds out that she can alter reality and has god-like powers, but you as player can only use her simple magic attacks and hexes. When she gets extremely powerful, she becomes the main villain.
The speeder character of the game called Bullet, he is the fastest superhero in the game and can do some short super-sprints, or has an upgrade where the short super-sprint can do a knock-back effect on an enemy. But he can't super-run at impossible speeds across the maps and catch all the criminals in the blink of an eye, Flash-style.
There are a few powers that are problematic to simulate in a game, even if all can be shown in some way. Superspeed (the super superspeed) and reality altering powers are two that even cause problems for writers in comics. Hence they "depowered" Franklin Richards and don't really have realistic superspeed stories. Hell they even had to (storywise for no reason whatsoever) cut out Quicksilver from the rest of X-menDoFP just because they knew his power could pretty much solve any obstacle or problem.
Below is mostly about supergroups and use of powers. For a single player power/hero it is easy to design the game and enemies around their power. the biggest implemention problem of any power is how it affects the story, not how it is used in combat. You always get the "Why not just use the eagles to drop the ring of power in mount Guldur?" problem. Because why can't your guys know the plans of the enemies when you got a telepath? Why can't they get that object of power when someone can teleport?
1. Reality altering. Only works as a story vessel. Personally I would skip it in a game, is silly anyway.
2. Superspeed. Just don't have it at Flash levels. There are many methods to simulate or put it in a game though, I can think up tree just right now. Otherwise just have a fast character (Spiderman style) who can dodge away and/or have more action points.
3. Telepathy. Telepathy is a problem for storytelling, gameplay-wise (combat-wise) it is easy to implement. If you want to have any sort of story you can't put telepathy in the players hand as they realistically should be able to pry information from anyone at anytime. Hence why they in marvel have invented silly things to stop a telepath like those helmets...
4. Invulnerability. Problem with this power is that it basically eliminates most enemies from being any form of threath unless implemented in a good way or having mostly enemies that can partly break through it. Like super-speed it needs to be limited or you would almost only engage with your invulnerable guy and let the others stand back. (Hm, lets hide Green arrow and Batman in the corner while I take everyone out with Superman!)
5. Teleportation. "Bioware has put a door that can only be unlocked later, everyone looks at Nightcrawler". Again, easy to put in combat with many ways to use it. But you know all those unlockable areas, saving the damsel in distress behind Darkseid (I am sure he kidnapp princesses). "Now that was easy" blink said.