In the recent FE update there is an epic screenshot of a hero leveling and having multiple choices to upgrade their abilities - including the "rare" Double Strike.
My suggestion is to have certain techs and buildings (and quests and everything else) influence the probability of particular abilities. For example a level 4 city upgrade could be "Duelist School" which has all the usual bonuses for a city upgrade, but also increases the probability of having the choice of "Double Strike" from 2% to 5%.
Likewise a random druid quest can increase the chance of nature magic abilities. The "Logistics" tech increases odds of Intelligence abilities. etc etc
If nothing else, please just expose the ability probabilities in XML so that modders can implement such ideas. 