Most of X-Com's challenge came from the insane hide-and-seek-style gameplay
Yes, and the enemy AI is very geared towards that and quite good at it. They know how to pop out of hiding, cap a guy, and get cover again, or hide out in a house/crashed ship and ambush you. They don't TEND to seek you out, but that'd put them at a disadvantage.
Also, JA2 has a fundamental difference from XCom in that dudes, good or bad, aren't nearly as fragile as in XCom.
The randomly generated maps tended to be a little too crowded
I don't know if I'd agree with this in regards to UFO Defense. Most of the maps there were fairly open. TFTD though, definitely. Cruise ships, for instance. Also sunken ships replacing houses on, say, the farm maps. sunken ships were far less navigable.