Merging them should be a last resort only after trying some other things with them. Going all the way back to D:OS 1's alpha I've been bearish on the ability point bonuses outside of those for skills. In the EE and 2 they have gotten a little better but I'd still like to see each point matter more.
Far as points to maximize strengths/minimize weakness goes, well that's the good thing about the system is you can do one, the other or neither. You could wear magic defense oriented gear on a warrior to compensate as opposed to leveling the ability, or you could let it ride leaving one of them weak.
If you combine them it creates a no-brainer type ability that everyone is going to want to increase when playing blind for the first time. I'd probably rather see them both removed outright than combined thinking about it in this way.
But first try making them have more impact and have each point invested matter more. A couple % doesn't do anything for anyone past that first investment.
