It’s important to note that these rules were originally designed to cover SAGA into a type of CoC game. The beauty of a classless system is that all PCs are as equal as possible you can completely disregard the rules of class balance and open the door wide open to the kind of characters they want.
Skills: Skills are most often extremely important in classless game and characters without good skills are at disadvantage. For this reason I generally give the maximum amount of skills in this case that would probably be the Savant.
Weapons Skills: It really varies depending on how much combat you want. Generally speaking the middle of the row option would fit the best. If you want a party of elite combatants than give your PCs the maximum most likely that would be vanguard. If you want to PCs to be weaklings than give them the combat skills of the savant or envoy. In my game the PCs were highly trained police officers and I gave them a lot of combat proficiencies, it worked out fine.
Talents: You can forget about class restricted talents and just open, however if a talent has prerequisites you must fulfill all of them. If a talent is restricted to a having a certain number of levels in a specific class ignore that requirement and substitute it with a character level requirement of that same level instead. Class level requirements aren’t important here, but you don’t want to give the PCs powerful talents faster than they could normally earn them.
Hit Points: In my game which was a horror game I gave the minimal HP (in SAGA that was the scoundrel), middle of the row might be better for most games. There is no reason why you couldn’t give max HP if you wanted to.
Defense Scores: Details here are dependent on the final defense system. In my original PCs had 3 defense points that they chose to spend on reflex, fortitude, or will. They could not spend more than two points on any defense score. If we go with a more 4.0 defense score method than the PCs simply pick one defense score to be their ‘good defense’.
Bonus Feat: There are two options here. In my game the PCs were cops so I picked out number feats related to police work that they could choose to spend their bonus feats on. It takes a bit of work, but it is not so bad. Option 2 is you just declare that bonus feats are just normal feats and let the PCs go hog wild.
