Hmm, cool idea for discussion -
* Not being able to romance Anarietta during B&W (the overall story arc was great for the main B&W campaign, just wish we'd had an actual romance side-story with her as I thought she was the most beautiful girl in the game and there were a few flirtatious moments between the two early in the main quest) - just found that very disappointing. (and yes, I've read the books, don't really care about her thing with Dandelion years before - I'd like to think after a good dude like Geralt saved her life and her country she might consider a closer relationship with a warrior type instead of a guy like Dandelion).
* The quest in Skellige with the lighthouse. When you come out of the Inn after Jorund is killed and the peasants confront Geralt when he was just defending himself from a bunch of punks - I wish I could've opted to wipe out the whole village if they'd decided to attack me instead of just surrendering and being taken to Madman Lugos - I thought that was just silly and unrealistic given Geralt's character, when the one guy says something like "you can't take all of us", I can just visualize Geralt going "mmmhmm....wanna find out?"
* The quest in Novigrad toward the end where you kill Radovid and then Djikstra thinks he's going to betray everybody and take over...I thought that was very unrealistic. Djiktra can be a jacka$$, but he's not stupid (quite the contrary, he's a very intelligent dude) and the last thing he would've done is try to betray Geralt's friends, and then think Geralt was just going to walk away and let him kill them, lol. That was just laughably stupid - should've been able to kill Radovid, and end things peacefully with Roche, Djikstra, etc.
* As a side note on this quest, I would have absolutely loved an option to kill Philipa Eilhart after the main game was over. I've wanted to cut her head off since Witcher 2.
* Agree with the OP on Maria Louisa - too small a part, and should've had a romance option there if you saved her son in Witcher 2.
* Another romance option lacking was during the Cerys quest(s) in Skellige - she flirts with Geralt all throughout the missions, would've been nice to have some options there as she is a pretty girl who is a very good person.
Prettiest girl I've seen with a scar on her face, hah.
* Better / more end-game quests would've been welcomed - quests with your selected Sorceress (if you chose one) where perhaps she simply travels around with you and you have added dialogue and cutscenes with her, quests to follow up on some of the characters you'd met during the main game like the Baron, doing a Witcher contract or two with Ciri (maybe heading back to the Bog to wipe out that last Crone together - that would've been AWESOME and quite fulfilling), checking on Priscilla as someone else mentioned, a follow up ending quest with Roche & Ves, maybe a quest to close things off with some of the Lodge members - I thought Fringilla had very little screen time given how close she and Geralt were during the books.
So ya...W3 is easily the best game I've ever played, but there were certainly some areas it could've been even better, IMO. I'd honestly pay for a DLC package for this game that added the aforementioned end-game stuff.