I feel the same with X3, it's my least favorite of the SNES trilogy although I played PSX version included in MMX Collection, which annoyed me more because of how slow all the dialogue is compared to SNES version. Seriously? What was the culprit behind the slow text speed? The SNES version can skip right through it no problem whereas the CD-based versions the dialogue's skip speed is slow as a snail. The Ride Armors, while interesting to more of them, but it's virtually moot since you never had to rely on them save for items if I remember correctly. I never liked the X-Buster upgrade in X3 either; X1 and X2's X-Buster upgrades made you feel more of a badass because the firepower of a fully-charged shot was straight to the point by charging your shot all the way. In X3's case, they do something in the veins of X2's buster upgrade by doing a "combined" charged shot. Cool in theory, but ultimately it's more impractical than it is cool and the damage you get out of it isn't that satisfactory.
Armor capsules in every stage is cool enough, except that most of the chips suck and once you learn about the Golden Armor they all become irrelevant.
The only chip upgrade I ever liked was the double air-dash chip to move around quickly, but as you said, once you know where to get the Golden Armor chip, everything else is pointless.