I went ahead and designed the alternative classes I was talking about. These can be used in place of the standard classes in most old-school fantasy RPGs and I believe even in D&D 3.x, along with some house rules that allow any character to use spells or gain talents/powers/feats.
General principal: GM rolls 2d6 and adds half the character's highest ability at the beginning of each adventure to get a current Class rank, which acts like a threshold; the Class penalty is = rank/6. It subtracts from chances of success. In applicable situations, if the character uses an ability that is lower than Class rank, then the Class penalty applies to the roll. Any time this effect is triggered, it's no longer a secret, so reroll one hour later.
A god or saint hates you. At the beginning of each adventure, your Damnation rank is the current level of holy outrage. Applies any time you ask for divine aid, deal with spirits, or perform ordinary actions on hallowed ground.
Like Damnation, but triggered by using scrolls, potions, or other magic items. If the spell fails, the Cursed character and a number of others = Curse penalty are affected by the reversed spell effect.
People don't like you. The Charm score of any NPC must be higher than Hatred or the penalty applies. In combat, all opponents with Charm lower than Hatred attack the hated character in preference to others.
You are terrible and untrustworthy in combat. Any of your followers run if their Charm is lower than your Cowardice. When you are attacked, you take extra damage = your Cowardice penalty.
Your plans tend to backfire. Whenever you follow any plan, your Foolishness penalty modifies the roll unless the ability used is higher than Foolishness. If someone follows one of your suggestions and the roll fails, they take damage = your Foolishness penalty.
You are frequently physically clumsy. If you use an ability that's less than your Oafishness, you get an Oafish penalty to your roll. If you miss an attack, you do damage to a random target = your Oafish penalty.
Sometimes, you seem destined to die. In combat or a dangerous situation, you take extra damage = your Doom penalty if the abilty used is less than your Doom.
Someone wants to punish you. Whenever you bargain with anyone, if their Charm is less than your Enemy score, they are working for your enemy. They may attack, capture, or report you; all future negotiations with them are modified by the Enemy penalty.