You should go for "increase ability level" on those heroes who's abilities have multi-target affect or stacking effects, I try explaining my point:
- AoE damage on a spell hits more targets ==> X increased damage applies on 5 targets ==> X*5
- Lumos's shield gives X resistance to your allies ==> every point is considered *5.
- Serafine's awakening skill grants X magic damage bonus on every spell cast. Giving bonus points there, you basically grant way more bonus as long as the fight goes.
Many heroes benefit on ability level, while others prefer penetration, flat damage or cc-resistance(e.g. Ezio)