First, clarification...all abilities can have a max of 4 levels...there is no difference (as far as the code is concerned) between a "normal" ability and an "ultimate" ability...it just so happens that for gameplay/balance reasons, ultimate abilities only have two levels...
If you want all abilities to be maxed out, then just have only 10 total levels....the original 3-3-3-1 worked fine...you also could do things like 2-4-2-2, or 3-3-2-2, or whatever...
It be worth pointing out that some abilities really don't benefit from having multiple levels....some abilities, like the progenitor's ressurection, really don't become any better at higher levels (simply having the ability to resurrect ships is powerful in it's own right)...some abilities, like the colonize on caps, could benefit from higher levels but in practice lvl 1 (simply being able to colonize at all) is good enough to serve it's purpose....some abilities (like targetting uplink) reach certain thresholds (being able to outrange a starbase) that once reached, serve their purpose and additional levels don't really do much good...
So, you could easily have a well-balanced akkan that has 2 levels of colonize, 4 levels of ion bolt, 2 levels of targeting uplink, and 2 levels of armistice...
Just something to keep in mind....in all honesty though, forcing the player to specialize their caps makes redundant caps (having 2 marzas, for example) more useful....