Morrowind's system was good in one way, in that it at least didn't feel like the enemies were scaling up to you the same way it did in oblivion. But the attribute multiplier meant you have to game your skill gains anyway, or end up with a worse character. But the difficulty of the game meant you didn't have to, so it wasn't so bad.
Even outside of level scaling situations, look at stuff like unreal world, or cataclysm DDA. Want to be good at throwing? Throw rocks at a building! That's fun for nobody, so why does the game reward it? But you'll be more effective if you do this boring thing, so from a problem solving perspective, you should do the boring thing.
Games are generally two things. They are puzzles to be solved, and they are entertainment. If the puzzle is too easy, the entertainment can be lost. If the puzzle isn't fun to solve, the entertainment is lost. Part of the puzzle of RPGs is how to make your character the best you can. If you add to your character by doing fun things with them, that's a fun puzzle to solve. If you add to your character separately from doing fun things with them, it's not a fun puzzle to solve. You find yourself trading effectiveness for entertainment, sure, you could be better at destruction magic, but who wants to shoot weak fireballs into the sky for 20 real life minutes?
This gets into the territory of earning your fun, a mindset most often seen in MMOs. Put in the "work" of grinding, then reap the "reward" of doing fun stuff with a good character. A good game should be entertaining at all times, at least in my opinion.
Fable's system was decent, but I still found myself playing to get the specific points I wanted, rather than just mixing up melee, ranged, and magic and using each where it was the most effective option. Still, it worked pretty well, but I think it would have been even better with just a straight point buy system.