That's why people exploit it so much......
Some people might. I doubt that all do.
But the main thing here is that it's irrelevant whether
anyone on the planet exploits it ("it" being vanilla levelling anyway, and so...) It's all about what the levelling system could be intended to reflect, and how well (and in what ways) it apparently does so.
Using skills, then directly receiving *associated* benefits (including increases in the skills themselves) is, to some at least, more "roleplaying-friendly" (or "immersive", or "supportive of verisimilitude" if you prefer
) than using skills, then "shopping" for whatever you as a player might prefer for whatever reasons, all over the place perhaps.
Anyway, I've been using nGCD + Progress (+ FCOM, et al) for a while, and that has worked well for me. One day, I might experiment with Realistic Levelling, just for a[nother] change. Previously, I have also enjoyed KCAS, and a few others. The best way to find out what will work for you, is... to find out what works for you.
Really, just try a few (generally, one at a time!) and discover your perfect system.