Star Ocean: Till the End of Time
This. A thousand times this.
I had just finished Tales of Symphonia. I usually don't get into jRPGs, but I really enjoyed the combat in Tales of Symphonia and I wanted something similar. So, I picked up Star Ocean: Till the End of Time. The storyline is completely incompressible. And I don't mean that its "trippy" or "post-modern". Without spoiling anything, the first 2/3s of the game are basically long versions of a Star Trek "Planet of the WeeK" episode and have no bearing on the overall story. Then, you finally get back into the primary story, except that a twist occurs that renders everything before it meaningless and ultimately ends without much explanation. I heartily recommend reading the Wikipedia article. In combat you have MP and HP, attacks use either, damage goes to either, and if either one goes to zero you die. It makes combat boring and frustrating at the same time, which is novel. And the icing on the cake is the excessively complex crafting system that actually involves patents, inventors, random drops, and investments. I know the game scored well, so obviously some people enjoyed it, but I haven't had a worse experience in an RPG.
An honorable mention goes out to Deus Ex Invisible War. They simplified the RPG mechanics without improving any of the stealth or combat of the original Deus Ex. I don't mind simplification, as long as it carries with it improvements to other aspects of the game. But it didn't. Stealth is basically identical to Deus Ex, including the often ridiculously short vision of most enemies. Shooting was more accurate, but the unified ammo combined with the high health of most enemies made it a poor shooter. The levels are smaller, but they didn't populate them enough to make up for the size difference. It is a mediocre shooter with weak RPG mechanics and a so-so storyline.