The problem is that this isn't a "real world" example, it's just hammering the existing skills(of which I remind you I consider most of to be garbage in need of a rework as well) into a system that's not designed to hold them.
I don't deny that there are problems with at least some of the current skills. However, in my opinion, if the only way for your ability system to work is to throw out all the existing skills, that says more about problems in your ability system than problems in the existing skills.
Slotting the existing skills in showed that consolidating all elemental skills into one ability and splitting the so-called "Tactics" skills off from the others produces a system which gives lots of benefit for magic users and forces normal attack users to split points between their weapon ability and tactics for mobility.
Bunching all AoE skills into one tree, all DoT skills into another tree, all mobility skills into one tree... that does not make for a coherent skill set because instead of picking one ability set containing a lot of skills which has a little of each, now you need to pick 3-4 ability sets because of the one or two skills they each contain.
the system is no more convoluted than the current one, and I'd even say it's less so.
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Phoenix Dive was likely not a "Fire skill" originally.
If I had to guess it is the same thing that was with Rain of Blood.
In which... They are both "Skill combinations" that were moved to being vanilla skills instead of remaining for skill crafting.
That's a neat catch, you're probably right that they do seem more like the result of skill-crafting combos.
