Here's why IX's ability system is flawed: You're given minimal customization options, leaving you with little room to mold the characters, which is boring.
Also, you learn abilities by wearing specific equipment. Your stat gains at level-up are also affected by your equipment. This becomes a problem, because if you're trying to learn various abilities (which you should be) and you level up, there is an amazing chance that you didn't receive the optimal stat gain. Too much micro-management is required.
Furthermore, if you want truly optimal stats, you have to play a Level-one game(which isn't entirely possible, since you're forced to take XP from three encounters in Pandemonium) all the way to the fourth disk, until you have access to equipment, that will provide the best possible gains. This is also a problem in VI and VIII, but with Espers and GFs, not equipment. The fact that Level-one games in IX are incredibly unfun and RNG-based, often requiring resetting, is painful. You can kinda trust me on this, considering I actually laid the groundwork for the FFIX low-level game, and receive credit in the LLG FAQ on GameFAQs.