Stuff you dislike about the EU?
For me personally would be the following:
Rakatan Empire, Kwa, pretty much any pre-Republic era race. The thing with Precursor races is that it really doesn't fit with Star Wars, and the Ancient is better idea is really cliche. Good thing that they didn't just flat out make those species as being more advanced than the Republic and Empire. Celestials I'm iffy on, I rather them be just force exclusive rather then them using technology.
TOR era. Note that this doesn't include KOTOR or TOTJ, although I assume most people know this. TOR story is pretty weak, it's just a mesh of a bunch of stuff that already happened in the EU and movies. Heck, if Dark Empire was written when we had a much clearer definition of what a Sith is the whole thing would pretty much resemble Vitiate's Sith Empire, since that's how TOR Sith Empire is written except they freely call everyone with a Lightsaber Sith.
TOTJ era. This stuff is pretty forgettable even though I know a lot of people seem to think it's some of the better stuff from the EU. Honestly I don't see what's so great about it. The majority of the characters don't do anything and just die in a later issue. Most of them aren't really memorable either outside of Qel-Droma and Kun and that's simply because they had the most time shown in the series. Kun and Qel-Droma came off more as bullies rather then actually advancing with their plans, Droma and Kun have really dumb reasons why they turned to the Darkside. All in all it's not that great.