The Alpha Skill system is far too front loaded. The class you take at 1st level is far too important. If you get rid of ranks so that the number of skill points you get at each level is irrelevant to your class then the number you get at first level also has to be irrelevant.
The following system removes this problem but as with all these no-rank skill systems, it isn't compatible with 3.5 but rather possible to convert 3.5 to it. This probably rewards massive multi-classing too much as well and may well need someone to come up with some restraints to add to it, maybe just making the bonus skill reward be based on class level instead of character level.
Untrained* (rank 0): 1d20 + Ability mod.
Trained (rank 1) 1d20 + Ability mod + 0.5x(character level +3).
Expert (rank 2) 1d20 + Ability mod + 1x(character level +3).
Master** (rank 3): 1d20 + Ability mod + 1.5x(character level +3).
*Some skill uses can't be attempted untrained.
**Mastery requires a feat to raise a single skill from expert to master. Feat can be taken multiple times.
A character starts untrained in all skills apart from their class skills in which they gain a non-stacking +1 rank bonus (so all class-skills start out trained before you spend any points, that's +0.5x(CL+3) ). When you multi-class new class skills also get this 1 rank step bonus, but if you get the same class skill multiple times you only get the bonus once.
All characters regardless of their class then get 4 + int mod skill choices at first level and gain an additional skill choice at 2nd level and every 2 levels thereafter. These can be spent on any skills (including cross-class skills) to raise them one rank step. You can add a choice to Rogue Talent class feature allowing them one additional skill choice.
Reduce the class skills lists to just core abilities, others can still be bought as needed.
Rogue class skills: Appraise, Climb, Deception, Disable Device, Disguise, Escape Artist, Knowledge (engineering, local), Perception, Stealth, Theft, Use Magical Device.
Fighter class skills: Craft (weaponsmithing, armoursmithing), Handle Animal, Intimidate, Knowledge (dungeoneering), Perception, Ride, Swim.
Wizard class skills: Appraise, Craft (alchemy), Fly, Knowledge (arcana, planes), Linguistics, Spellcraft.
Cleric class skills: Diplomacy, Heal, Knowledge (planes, planes), Linguistics, Spellcraft.
Ranger class skills: Climb, Craft (bowmaking), Handle Animal, Knowledge (geography, nature), Perception, Ride, Stealth, Survival, Swim.
Paladin class skills: Diplomacy, Heal, Knowledge (nobility, religion), Ride.
Some skills were merged because of the skill rank system and their not being enough points to go around so people always bought the best skills, with this system you should consider not merging some of the non-rogue skills. Use Rope, and Jump in particular might work in this system.
