My biggest complaint has got to be research and pacing. I got the research done to go to mars before I ever got power armor, plasma weapons, or even the avenger. Of the original aliens, I've seen chryssalids, snakes, floaters, and ethereals. Cyberdiscs, reapers and sectoids. I haven't seen a muton, silicoid, and possibly others? I didnt see chryssalids until november, floaters in september. I can't recall all of them. I keep getting MiB missions, when they are really nothing more than an annoyance.
I LOVE all the new races, while I know you aren't responsible for their existence, it is really nice to have so many. But researching most of them seems to be pointless.
And to go along with aliens, spitters seem to have at least three different corpses. Only one of them gives you the UFOpaedia insert, the rest do nothing.
A lot of the research seems to just be fluff and filler. Trying to figure out what is needed to research certain weapons is annoying. I got the stun launcher researchedz but never did figure out what gave me the research for the stun bomb. And stun the crap out of everything! I usually bring back at least 80% of the aliens on a mission alive. (Selling live aliens nets twice as much as dead with that mod on.)