What kind of rules beside weapons modules do you mean?
Some rules need a replacement to not be overpowered, including weapon modules. This is how I create a higher-powered but not necessarily indecently powered game, in order of importance (of what I have listed anyway).
1) Remove or modify ALL existing organisations. If there is one thing that stops Anima from being a story of superheroes it is that there are 6-10 organisations of people 10x stronger, some with nukes and lazers, that say, "No! No supernatural stuff on our watch".
This is definitely the most important thing, the setting has to be changed because it is designed to be low-powered.
2) Decrease the rarity of magic items. As with #1, the setting is the main thing lowering the power in the game, and this is no exception. Increase the maximum quality bonus all metals can be crafted into by 5, decrease the difficulty of crafting such items. Make "Artifacts" much more common, including things to increase Magic and Psychic Projection, and things to increase the size of Zeon Pools and Psychic Potential. There is too much in this area to do to go over in this section...
3) Give the choice of [Use of Ki and Ki Control] or [Use of Nemisis] as a free ability to everyone. Make 'The Gift' and access to Psychic Powers cost 1CP instead of 2. The begining investment into Ki, Magic, and Psychic abilities are high, so make them cheaper. Giving The Gift or Psychic Powers away for free is too strong, but making them 1CP makes them much cheaper without allowing everyone to have them.
4) Weapon Modules. Replaced with: All Fighter and Fighter/Prowler archetypes start with 2 Whole Class Weapon Modules (such as Barbarian, Ninja, etc). Prowler, Domine, Novel, and any other half-Fighter archetype (Fighter/Domine or Mystic or Psychic) start with one Whole Class Weapon Module. Anyone else (which is just Wizards, Mentalists, and the like) get one weapon as per the original rules. All weapon Modules are also cut in half in price (Weapon Masters get them for 1/2 that).
5) Costing DP to switch classes, this is low powered in general. A few classes can become stronger, but it normally weakens or at least just displaces skill instead of becoming stronger.
Replaced with: Needing a thematic reason to switch classes. If the story makes sense they can switch, but this is obviously up to the GM, if it is just for mechanical benefits they shouldn't be allowed to do it.
6) There is the option of giving more CP. This is the easiest and fastest way of increasing the power of the game. However it is also dangerous, giving even 1 more is a lot more power to everyone. I wouldn't give more than 5 unless I wanted an extremely powerful game.
I know there are more, but I can't think of them at the moment. Also, remember these are all HOUSERULE options to purposely increase the PCs power. They are most likely not completely balanced, but this is intentional.
EDIT: The more I think about it you really would not have to change the rules at all. All you have to do is change the setting. Add more tolerance to the Supernatural and more magic items and you have instant high fantasy. (Also known as Instant High Fantasy, just add Magic.)