Re: IC and discussion- game about summoned powerful heroes
If I might offer my thoughts I think you're essentially trying to decide if you want to do the work up front or in the back end.
What I mean is this:
Freeform: Freeform, you have to take a hand in establishing the power level the players are entitled to when you let them know how to complete their RTJ. I don't personally see that as difficult. You can say things like "Your character should be able to handle a cadre of soldiers by himself but can't stand against an entire army." or "Your character should be the sort of whom dragons are wary and even ancient evils know to respect." and so on. You find the tone you like. You can do the super-hero thing if that's easier for you or you can pick characters from anime, movies and so on. "Your character should be roughly as powerful as Leonidus from 300", "Your should be more like Daredevil than Spider-Man."
You get it. The key is when they apply, you have to review what they claim their powers are and then decide if that works. And then be willing to say "I see your character is a bloodmancer? And that they can create and shape the blood of anyone they touch, but that's a bit too much. What if they can only affect their own blood?" or whatever you want to say to someone who proposes that. You can regulate the characters power. You can tell them they can fly as fast a hawk on the wing but not as fast as a plane.
You have to do the work up front establishing the character's limits and of course Freeform isn't perfect you may have to kindly regulate overtures and such.
D&D/Pathfinder/System Game: This one is a bit easier upfront. The system regulates challenge, and danger and power and abilities. Its becomes very easy to tell your players "Make 9th level gestalt characters" or "Everyone make 12th level characters but you can have 2 bonus feats." And they put together those characters and you look at their sheets and because the game is formulaic it's not that much work to look them over to make sure there are no gross exploits or miscalculations.
But in exchange it can be restrictive. You want to run a Nine Headed Dragon God made of the corrupted water of life. Well now you've got to jury rig an existing monster together and give it stats. Because if you run a d&d game and you spend half of it saying "Oh, his AC is just tooooo high for you" people get frustrated. Because d&d is clear on its rules.
Similarly, you have to run mechanics for almost everything. Player wants to seduce this noble woman and extort her for her secrets. Skill rolls. DCs. Circumstance bonuses. They want to pick a fight with the grand knight. What level is he? What are his stats? You'll have to come up with them so they can roll out this fight.
d&d can make a great framework and it keeps everything mostly level and fair. But it cares a lot about exactly how many feet away someone is and just which type of armor they're wearing. And it limits what players can play and do. A wizard gets x spells a day. That's it.
Summary: My opinion and advice is that if you want a high-fantasy wild ride colourful game full of exciting and interesting characters -- essentially higher fantasy/anime-esque content, then go Freeform. You wont be tethered to the system when it comes to magic, spells, abilities, and content.
If you crave the structure and order of D&D, use that instead. It will narrow the scope of what can be (without house ruling and working around it) but it makes it easy to put together a group of 9th level heroes and throw them in a room with an adequate challenge. And it's easy to know when a fight is won or lost because the rules and dice handle that very cleanly. There will be far more bookkeeping though. Hit points. Initiative. Distance. XP. Treasure. Giving out adequate magical loot (D&D characters can be very gear dependent, especially in 3.5/Pathfinder).
As a writer, I personally prefer freeform. But it's whatever you think fits your style that's going to matter. I find mechanical games can get bogged down in well, the mechanics, if you're not careful.
If you run a D&D game, they'd have to be high level to feel sort of like the paragons you're thinking of.
You could maybe run something light like Window or Fate if you need a system.