Pretty much all of the Megaman Battle Network (Rockman EXE) games had random content removed from them. Boktai linkage, etc. The 6th one actually had an entire extra area removed, for presumably no reason.
The Megaman Zero games had blood removed.
There's also weird cases, where you could consider the US version worse by having more stuff added to it:
Dragon Quest 8 on the PS2 was (in my opinion) slaughtered for it's US release, and barely has any semblance of a DQ game. I'd love to play the Japanese version of this (in English) someday. Great synth music, no voice acting, and the simple menu's. No accents in the script would be a plus as well, and the old item/spell names. I'd actually like to try doing this hack myself, if I ever actually get to that level...