yeah lesbian undertones were obviously a bad thing and almost ruined those episodes for me
but seriously, most people hate them for being slightly more serious than episode 1 (which is lightheartedness incarnated since that's Imaishi's specialty) or for "being Eva all over again", which is the most idiotic thing ever. The direction's kind of Anno-ish during some parts but it never gets even close to Eva's pretentious emo bullshit.
And the ending was actually conclusive and well done for a change. I didn't put it past Gainax to take a crap on Go Nagai's classic work with a GAINAXEND, so I was pleasantly surprised