Well i haven't read the books yet, so i don't really know how a lot of these differ in the books... BUT! This is one that I've heard about - for one thing, i know that Jamie didn't even come back until AFTER Joffrey had died. More importantly though, from the multiple articles I've read, as well as talking with the ultimate fan of GoT - aka XxXRachellXxX - i know that in the books, it wasn't really Jamie forcing himself on Cersei [or raping her, which is basically how it played on-screen.] From what I've gathered, the encounter started out with Cersei initially a little resistant, but she soon changed her mind - without undue force or coercion - and was completely willing, consenting, and enjoying their sexual encounter...

This was too quick, I think it was obvious they didn't have much screentime for it. It's annoying that they made it such a big deal in the promos and finished it in a minute.
I don't think that Jaime and Cersei scene should have been there at all.

It felt so out of character and completely unlike Jaime. It also really annoyed me because they're my favourite couple:/

Only this one and Asha's. The first one is pretty skewy and not at all like in the books (also a big character derailment moment for Jaime), Asha's was just a joke and a waste of screen time. I remember how the promos seemed to suggest that Asha would have a lot of scenes this season and look, just one miserable scene. And next season the Greyjoys will be omitted. It'd be funny it wasn't so frustrating.

Also Asha/Yara, and the shadow assassin.