What I miss is the freedom the original game offered you. It didn't tell you 'you have to choose between these three missions.' If there were three abductions or crash sites, it was your choice if you wanted to go for all of them or just one. One would think the earth's largest defense initiative would have the initiative to keep more than one skyranger so they can deal with as many threats at once as possible, but clearly not.
I also miss multiple bases and having unit 'classes' determined by the equipment I assign to soldiers and not soldiers being limited to certain weapons based on an artificial class.
All in all, it's a pretty good game, but not one I'm ever going to play again. Compare that to the original X-com which I still play to this day.