First up, let me say great effort. That being said... I've got a comment.
Set Hit Points
If we don’t roll to gain other level dependant benefits such as skill points and feats, why should we roll for hit points? Using this variant, characters gain half their hit die plus one hit points per level instead of rolling their hit die.
Errrr. Wait. That gives a character 210 free hit points over a 20-level career, regardless of class. Meanwhile you're taking away a half hit point on average from the die roll. Average over time for a D12 is 6.5 Average for D4 is 2.5 Your system shaves the halves. Which amounts to 10 hit points on average over the career. Net result: +200 hit points.
Even if you're eliminating hit points gained/lost from having a Con bonus/penalty, that's still a pretty steep power-creep. I would think a melee type who puts reasonable effort into his Con score would probably pull maybe as much as a +7 bonus by 20th. So +140 hitpoints for him from Con.
That means a fighter type stands to gain 60 hit points for free with your house-rule. A wizard who's got a decent chance of having no meaningful Con bonus (let's give him +2 just to be generous) would accrue 40 hit points from Con, netting such a character 160 hit points for free.
I'd think that's pretty serious. If you're not taking away hit points from Con, it's even more serious.