I always wondered how the UFOs disappeared from the geoscape after getting shot down; presumably, another UFO can come and fix it ;-)
Larger maps do equal longer, slower games: I am happily ignoring the long campaign based traditional XCOM game in favour of just the battles ;-)
The best XCOM/TFTD versions (imho) were the demo disks for PC - no geoscape, just 1 battle with a random (well, preselected, but pretty mixed) selection of equipment against a terror mission/ UFO of some sort.
The large maps of TFTD did mean it can be irritating to find that last hidden Alien - one aspect of TFTD I can live without.
The plus side, however, is a more immersive battle. Terror missions have a feel of being in a large city; tactics need to change (cannot cynically exploit "edge of battlescape" for flank security, nor form "one big line, sweep left to right"). It means Aliens can flank; need to keep looking back, too. It becomes more important to bring enough ammo - no more flatten everything, as that exhausts ammo. It forces you to storm, or avoid, farm houses / buildings. It also stops the old, and now a bit boring approach, of sweep clean the surroundings and then storm the UFO - on a sufficiently large map, you cannot clean out all the aliens so easily. It makes using blaster bombs fun, too; lots to shoot...
There are some other nice aspects too: need to send out lone scouts, try and find UFO(s) or aliens; avoid conflict until you can get sufficient strength of numbers to make it practical. It means it could be possible to get cut off from your transport - no guarantee of easy retreat. It also opens up the possibility of unwinnable missions - where there are simply too many aliens to kill them all, but you could still steal new alien tech / capture aliens / destroy some artefact even without needing to kill all the aliens. Of course, you need to get back to the evacuation zone... I also found alien bases to be a bit sparsely populated. Much more scary if there are 50+ in there!
Finally, a long mission is a good chance to dynamically alter lighting - a day / night cycle. Night falls.. and the aliens come for you!