Glad to hear I wasn't the only one having a bitch of a time with the UFOs in this game. I had to actually exploit the save feature just to get all 7 Time Stones.
A few other things I noticed:
* The 3 bleeps that play when Sonic is underwater before the countdown are now from Sonic Generations, replacing the original sound effect. In addition, the 5-second countdown doesn't start making sound effects until it gets to 3 now.
* If you get more than 9 lives, the counter actually displays them now (i.e. 12 lives), as opposed to just 9. In addition, the game automatically saves your lives and score now after every Zone/Special Stage.
* The water automatically drains in Tidal Tempest Zone 3 after you beat Eggman, even if you push to the left. I assume this is to prevent killing yourself after the boss fight.
* You can no longer enter your initials in Time Attack, which sucks.
* Speaking of which, in Time Attack in Stardust Speedway Zone 3, you no longer rescue Amy after your battle with Metal Sonic. You destroy a capsule like in the first 5 Rounds' third Zones.
* The sliders in Wacky Workbench now make a sound; the same sound used for a charged-up spring in Sonic 2's Casino Night Zone.
* The font for the endings after the credits is different now and much bigger. The "Presented by SEGA" message also no longer appears after you beat the game.
* The How To Play section actually has a somewhat accurate storyline from the Japanese manual. No pictures of the enemies though, or even their names. (They still use the original English names for items, like Shield and Super Ring.)
* You have to wait for the music to end after a Zone or Special Stage before the score is tallied up. Since the U.S.'s version of this music is longer, it makes it more annoying.
* No Debug Mode at all in the game (which isn't a surprise, considering it was removed from the other XBLA ports of Sonic games).
* Tails is playable, but you can't see the opening/ending animation with him, or even the original credit roll. He can fly and swim like in Sonic 3, and his sprite is a modified version of the one from Sonic 2. (His flying sound is the same as Sonic 3's.) He can still kill enemies with his tails, but he can't harm Eggman in the boss fights, nor can he destroy Eggman's machines in the past. Amy does not appear at all in Tails' game, though the past machines, Metal Sonic holograms, and Special Stages are all there for Tails to tinker with.