After a while of playing i found that available xp for exercising skills decreases to zero quickly after gaining it. It means most skills don't get excercised unless you usually use them right after fighting.
I hacked my version to randomly deny a skill exercise if you don't have much available xp. The chance is available xp / total xp needed this level. Seems to work well - skills are getting exercised more evenly and it finds its own equilibrium. You can still do something repeatedly to practice its skill, just you don't have to do it immediately after killing a powerful monster.
patch to source/skills.cc
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I definitely think we should try this -- the idea shounds highly interesting. An opportune moment would be when we have not changed much stuff related with xp and skills (this is not now, post 0.3.4).