Just a quick thought. If you liked the quantity of skills in Alpha 1 and the granularity of skill points in Alpha 3 you could create a hybrid like this:
Use the Alpha 3 skill system and give bonus skill points equal to character level.
1.) You end up with roughly the same number of possible maxed-out skills at a given level as Alpha 1.
2.) Class levels still matter after 1st.
3.) You get to keep the granularity of skill points.
4.) As a DM you can still quickly eyeball the number of maxed-out skills when creating NPCs, even using the Alpha 1 rules if you like (though with the simple class/cross-class mechanic of Alpha 3).