I take it as obvious that an indie could never get the IP, but I'd be so much more excited if this was going to be a saga featuring Dr Bruce Banner, (starts singing) 'altered by gamma rays, turns into the HULK'.
Could have a skill point system that was similar to classes, and still be simple. Can put points into Bruce, Green Hulk and Grey Hulk skill-trees (Professor, Demonic and World-War-Hulk versions of the Hulk are prestige classes available only through combinations of skill, alignment, quest outcomes and plot events, e.g. playing goodie-two-shoes with emphasis on Bruce, choosing all the intellectual solutions, but still researching and going Hulk SMASH at the right times eventually allows Bruce to take control of his rage, allowing the Professor Hulk, where he retains the full intellect of Bruce and also gets a strength somewhere between Grey and an angry Green Hulk).
Points into Bruce give intellect (starts out smarter than most - a D&D 15/16, and about on the level of Iron Man), and can eventually make him into the smartest guy in the Marvel universe, overtaking Reed Richards, Xavier, Dr Doom, Dr Strange etc. It also decreases the likelihood of raging and forcing combat (i.e. turning into the Hulk), and when the Hulk (whether Grey or Green) he has a better chance of getting the Hulk to act reasonably rather than just randomly smashing whoever is near, represented by a greater number of action points per round.
Points into Grey give cunning and insight. They make it easier for Bruce to learn the nature of his inner demons (giving perks such as the ability to transform in return for a cost, and eventually at will). Has a morality penalty if he starts doing too many things that are not in his interests (may make unavailable an option to accept a quest if there's nothing in it for you. Increases the strength and hp of the Hulk (again, regardless of which version of the Hulk you happen to be - i.e. works as a % bonus, so green hulk will still always be stronger than grey), but by considerably less than if you were to put points into green instead. But most importantly, opens up the skill chains of stealth (yes, for quite a long time there was a period where the Hulk in grey form was only slightly larger than a normal human, would wear clothes, do underworld 'jobs' (taking control of the body for months at a time and directly setting things up to provoke Bruce into changing straight back if he unexpectedly turned back to Bruce - and he did creep around as grey, not just smash shit), intimidate (obviously you're intimidating everyone in green form, but you can only speak as Bruce or Mr Grey, unless you've unlocked a prestige class) and observation (identification in dialogue and by visual cue of non-scientific things that Bruce would miss - especially things to do with crime and the seedy underside of life, that Bruce would miss if not for Grey's influence. Lastly, enough points in Grey are needed in some situations/conversations to discover the existence of some prestige classes (particular demonic).
Points into Green massively increase the bonus to strength and hp in all 3 forms (plus any prestige form). High investment in green leads to times where you will auto-initiate combat by changing into the green hulk ('don't make me angry...'), and other times will open up (or even force) 'angry' responses ('you broke that on purpose you useless shit!!') if in a form that can talk, like Bruce, Grey or World-War-Hulk form (I'm guessing that high investment in green would be inconsistent with the Professor prestige class). They open up skills enabling change of body size in any form except for Bruce, fast travel via giant-hulk-jumping, and faster in-combat movement via small-scale version of the same (hence lower action points is partially balanced by being able to do more with what you have). Ultimate perks gained by investment in green include the ability to auto-change into green hulk (or any prestige with equivalent immunities) if you would otherwise be killed by anything that green is immune to (lack of air/vacuum, poison, etc), and upon any blow that would kill you if you were in a less powerful form - downside is a greatly diminished control over changes, so you change to Green whenever provoked (e.g. a possible combat, even if you could have avoided it through Bruce trading scientific skills), and then back to Bruce once Green has finished the combat (preventing controlled changes to Mr Grey).
The actual form you are in is independent of the skills (except that the skills can make it easier/harder to change into particular forms). Bruce the best with science, polite society and strategic planning. Grey is best with cunning, stealth, haggling and criminal dealings - is superstrong, but his strength and hp are fixed by level and skill investment. Green cannot verbally communicate, provokes hostile reactions from armed civillians (which may lead to hostility against Bruce if a change is witnesses), can fast travel at will and has three massive combat advantages: (a) highest per-level/skill strength and hp, (b) an anger meter that gives further bonuses to strength and hp (all other forms except WWH lack this anger meter bonus), and (c) a hefty list of immunities (as mentioned above). Professor has all of Bruce's skills, conversation options and intellect as though he was Bruce, plus Green's pre-bonus strength and hp, but no bonuses from anger. Demonic is the same except substitute Grey Hulk for Bruce (so all of Mr Grey's abilities and conversation options, with Green's combat stats minus the bonus). WWH is Green (keeps the anger meter and bonus) with the ability to verbally communicate (still gets hostile reactions from civilians) and a smattering of skills from Bruce and Grey (e.h. has Bruce's skill with science and Grey's knowledge of the underworld.
Crap. Now I want this game to exist outside my head:-(