Bad: Terrible camera control when it's in a fixed position at night,
unresponsive controls when trying to press the A/B/LB/RB buttons perfectly timed,
Sonic slides too much and turns too slowly during the day,
the HUB has the most boring/redundant/tedious/pointless NPCs and missions I've ever seen,
finding all 400 Sun/Moon medals without a guide was extremely frustrating,
Eggmanland was not beta-tested completely,
some ledges and handles that could be locked-on to had tiny windows for error (which leads to more proof in a lack of beta-testing), and
the hot dog missions were frustratingly repetitive.
Highly amused that very few of these exist in the Wii versions.
At least in the Wii version, I almost never had camera problems at night ... with very few exceptions, the camera pointed exactly where I wanted to go, and if Sonic was behind something, it would turn invisible. IIRC, there were a couple of places where the camera was deliberately the issue (like an item box or two that would have been really obvious at other camera angles) but nothing serious.
Quick stepping isn't too bad (I would guess that's what you're referring to here) but it was kinda odd with Wiimote+Nunchuk: you held B and tapped the control stick. Oddly enough, B on the Wiimote actually served as a cruise control - once held, Sonic would run straight forward at top speed. Now that I'm used to it, I think it's a useful mechanic that could work in future games.
I don't know what you mean by "slides too much" but I prefer him not turning much when running that fast. It's easier to not fly off a cliff that way...
Wii has maps, not hubs. Yay. Conversation is pointless (particularly the fact that every time you have a decision, the correct response is ALWAYS the first of the two) but can be skipped quickly. Oh, and missions are NOT NPC generated.
All Sun/Moon medals are awared at the completion of the mission, and awarded by rank/success. S-ranks for night levels are absurdly easy if you know what you're doing (I typically get them on the second or third run of the level, given that the first run I spent 10+ minutes on each looking for items). Item boxes, however, are scattered throughout the levels, but there aren't many of them and they're usually found in shortcuts and hideaways. Having a map in the night levels helps too.
Crimson Carnival didn't seem to have any glaring glitches that I was aware of. I still hate whichever SEGA employee came up with the idea of that one path that slopes left and right - it should not be something I'm likely to die on at all, yet have died on 20+ times by now.
Ledges and handles are best done as Paraxade said, and I think this holds for both versions. My method of choice is pressing and holding the grab button (B for Wiimote, X for Gamecube) and using the jump button (always A) to let go of an object. The instant a ledge is targeted, Sonic will grab it. Even better - this way often is very forgiving; let go of a pole too soon and you actually have a very good chance of grabbing it again.
Extra missions aren't often all that repetitive, but IIRC there's a lot fewer of them on the Wii version. There are also some real gems in these; the Spagonia time trial mission was a real surprise. Though I really wonder why they didn't just use that mission as the primary mission....