... First, diagnosis of the problem - make every race more-or-less viable in every archetype. Having races as they are with only adjustments for upbringing provides too small a difference to make the underdog choices viable. And picking your own stats Ethelon-style is too confusing for real newbies and offers too much area for powergaming.
....

I have recognised the goal and the key to reaching it. Now we have a problem - powergamers would use the new system to pick uber build/race combos, being even more powerful than before. My solution is simple - we have to first recognise what are the most powerful races for each guild with the current system (specced Faeling, Mugwump, Aslaran, Krokani and whatever else), then make sure the stats attainable under the new build/race system cannot exceed stats of these races pre-change. That way we won't improve the "best" races, only the bad ones:

I think it would be cool if you could choose bonuses to gain at certain levels based on your race or guild, though. Maybe have something where you choose at 1/25/50/75 from a trait or two.

Say, for example, the Celestine track looked like:



And the aslaran track looked like:



You would have two options at level 1, three at level 25, three at level 50, and three at level 75. Some would focus on their guild and gain powers based on their guild, some would focus on their natural abilities and gain powers based on their race, and you'd have a wider range of playstyle