I would use (unsurprisingly to some) 2Ed AD&D as my core. Then I would murderlize the shizz outta that. First I would take the business end(up to your personal tastes which that is) of a plunger to the magic system. I would reverse the backwards D&D math (do you hear me THAC0? Imma comin afta youuuu!) and alter the optional proficiency system to be a skill system where (Gasp!) your characters actually improve. I would base Hit Dice on race as opposed to class.
While I was at it I would find a simple way to incorporate the fact that your armor gets beat to HELL!! when you get mauled by a ravenous Orc wielding a double bladed axe!
Oh, yeah all that trauma that was done to wizards for the sake of “game balance”? GONE bitches! At level two in my clone you could actually cast…wait for it…SECOND LEVEL SPELLS!
Rogues? You wanna know about rogues? How about codifying the thief skills into the new skill system? Yeah! Yeah! okay well how about making their attempts to backstab REALLY count?
Okay….calming down now.
Boneyard 
I’d like to see a retro-clone system that takes both race and class into account when calculating Hit Points.
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so with skills retro thing how good is a one in handgun????? and do elves still get a +1 to sword & bow????? nuttin but luv man….nuttin but luv
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I changed over to a points based system [essense] for magic in our AD&D game. I also created a higher point based system for higher level magic [runes] that doesn’t really come into play until you are at least 14th level.
Both systems allowed for more abstract use of magic in the game. Some examples from our campaign are recharging magic items, “action points”like effects for essense cost, taming animals, improve relations with the Fairie Court, cause magic items to overload and explode, control portals, etc.
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