If one group enjoys to play a bunch of superheroes^2, IMO it's not the role of the game to tell that group that they can't do that.
Go play a different game. There are systems built specifically to cater to those kinds of games.
Psion (play a god-child). It even has three different core books for three different levels of play: Hero (i.e. Xena*), Demigod (i.e. Hercules), and God (i.e. Zeus).
GURPS (supports fuckall and then some)
Marvel Heros
Heroclix
*Debatable example. Hercules is clearly demigod, as per the definition ("half-god"), so its hard to find a good "hero" example.
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As for what you specifically mention:
You can only have 35 BP worth of positive qualities. - Pointless limit IMO. If you want to spend 100BP on positive qualities, that's 100BP you aren't spending on something else.
You can only have 35 BP worth of negative qualities. - Fair enough that you can only get a bonus of up to 35BP, but feel free to take more if you want them for character reasons.
You can only have 35 BP worth of positive qualities. - Pointless limit IMO. If you want to spend 100BP on positive qualities, that's 100BP you aren't spending on something else.
You can only have 35 BP worth of negative qualities. - Fair enough that you can only get a bonus of up to 35BP, but feel free to take more if you want them for character reasons.
Both of these limits exist in almost all game systems. There are only so many flaws you can take before the character becomes unplayable, unrealistic, or a bane to the group as a whole ("so wait, you are Hunted, have an Archenemy, and your a clone, AND your a blind quadriplegic? Not only do you have three separate 'big bad' level entities after you, you have no ability to defend yourself.")
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You can only raise one skill to 6, or two to 5, the rest must be 4. - Pointless limit IMO.
Skill groups cannot be raised above 4 (see above). - Pointless limit IMO.
Skill groups cannot be raised above 4 (see above). - Pointless limit IMO.
Enjoy having no room to grow. You're already to the best there ever was. Thought about retirement yet?
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You cannot have more than 6 essence worth of implants. - Pure game balance issue. Fiddly to deal with on top of that. Drop it IMO. If someone wants to play a cyborg, let 'em. And no, I have no problem with the cybered up mage either.
A skill can not be augmented more than 1.5 times its natural rating. - I'd probably modify it a bit, but I can find a good in-game explanation for such a limit. After all, you can only press the human(oid) body so far, regardless of the augmentation, and there is only so much you can get a piece of machinery to do.
A skill can not be augmented more than 1.5 times its natural rating. - I'd probably modify it a bit, but I can find a good in-game explanation for such a limit. After all, you can only press the human(oid) body so far, regardless of the augmentation, and there is only so much you can get a piece of machinery to do.
You can only press the human body so far, but doing so doesn't harm your ability to be a magic-slinging demigod? Weren't we already playing Magicrun?
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I'll ignore the rest of your list, as it's related to a different sort of game, from what I can immediately determine.
Several other systems, actually. GURPS and D&D being notable.