3x3 Eyes doesn't have any FMV in it. You must think you are on the Sega CD forum.
As for differences, it's true that the AC does little to nothing on most of the games that have both ACD and SCD logos, but there are a few verifiable upgrades in ACD mode that I can think of.
3x3 Eyes: Night and day. In fact, this game might just be the ultimate ACD tech demo.
Gulliver Boy: I don't know what the deal is but the back page of the manual mentions something.
Flash Hiders: IIRC one character gets a voice sample added to his win pose. It's really pathetic.
Popful Mail: I thought it did something, but I can't remember. I don't have this game.