Hmmm... in terms of base and resource management, you might want to take a look at Dungeon Keeper 2. It's a very silly game, and knows it, but it was ALL about base management and construction, and did a very good job of it. You had minions to dig rooms and mine gold, you had to set up guard posts and traps, keep everyone fed and happy. Directly copying the setup wouldn't be good for an X-Com game, but some of the ideas are useful. How the bases are built, for instance, and being able to watch your minions run around doing their jobs as was mentioned before was always fun.
Yes, I know, long on rambling and short on actual ideas, but still.

One actual solid contribution that I would like is this: Have your troops visibly gain renown. If a guy charges into a room full of Mutons with a plasma gun and takes them all out, he should get a medal for it. If he does the same thing with backpack full of high explosive, he should still get a medal, though posthumously. If a lady walks out of your ship and comes nose-to-nose with a Reaper, and proceeds to blow it away with nothing but a basic rifle, she should for the rest of the name be known as Reaper Killer Tatynia or something (this actually happened in a recent game, which is why I mention it). It should keep track of your troops' kill/capture scores, and maybe also squads as a whole. It doesn't have to be anything big or fancy, just a few extra notes in their personnel files and an announcement (MAYBE short cutscene if someone gets a medal) at the end of the battle. Maybe Reapers get a slight morale hit if they're fighting against a squad with Reaper Killer included.
I think this would greatly enhance the effect of what Kekko mentioned: you would get attached to soldiers, make little mental stories about the battles. Everyone would be a minor hero one way or another, but the war is not lost if a hero dies. It doesn't have to be a big issue or feature, but I think it would make a REALLY nice detail.

I think that being able to select where you land would be an excellent addition.

Say that just before you land you are presented with a topagraphical overview of the area. You could then see what the area looks like and then pick where to land based on mission type.

If your mission were to recover alien tech, you might decide to land where you could approach the UFO from an area where you are covered by the rise of a hill. If you had to do the same thing where you had to slog thru a town and were forced to go door to door clearing out buildings, you might loose more men.

If, along the same lines, you were sent to protect a town, like in X-Coms terror missions, you might choose to land away from the town instead of right in the middle of it where you could be sniped by the aliens hiding in the buildings.

Oh, another thing! A monument or something with the names of all your dead soldiers... Or a graveyard, Or something!
Whith some info on their deeds. Kill score, rank, missions, etc...

I also think that UFO:Enemy Unknown (as I believe it was known in this country), was one of the best games ever.

Good:

- The Geoscape. "Realistic" build times, shipping times. So you want to ship 20 power suits to your base in New Zealand from England? It'll take yonks, during which time they aren't available to either crew :)
- Random scenario generation. How light it is is dependent on what time of day you land.
- Destructable things
- Base defence missions - you get to play your ACTUAL base which you've actually built up :)
- Research, manufacture. Economics. Elerium-115

Bad:
- Having to manually equip everyone at the start of a mission - it should be possible to create a "profile" for your squad. Say a few people have blaster bombs, everyone else has laser rifles etc.
- Generally poor UI especially in the geoscape screens (but the goodness of the geoscape itself compensates)

Ugly:
- The game crashing
- Having to reselect the snap shot AP thing every turn (GRR) (Fixed in TFTD, but it was a much worse game)
- Mind control - IMHO not a good element to the game. Doesn't help when your guy gets mind controlled and blaster-bombs his own side, everyone dies immediately. Gets really annoying later.
- Mind control - if your guys get good enough at it, it makes things too easy

This whole hero thing got me thinking ... take the old arcade concept of "high score" and apply it to your individual soldiers (the "war memorial" or some such - not the "graveyard" :) ... like when you loose a game of Civ III or whatever. But in this game, since you have mutliple characters growing, gaining, and dying, you are getting high score entries WHILE playing the game (when each decent hero dies), so you get the added emotion of a good high score, and the added sadness of the noted passing away of one of your best ever ... it would basically just be a game element to crystalize the emotion you already feel after a good character dies in a hard mission ... and even cooler, if good characters die in easy missions, or bad ways, you could get income penalties or other negative effects (a hero dying at the enemy hands increases public awareness and funding ... a foolish leader sending a squad to their doom, or a possesed private killing his own squad does NOT have the same effect on the public).

The tactical combat wasn't that different from the old C64 Laser Squad. What made it more interesting was the how it was connected to the the geoscape and all the things you could do there(in geoscape). Research was pretty interesting, I remember being awfully curious about what I would discover about the aliens and what kind of technologies could emerge.

At some point I lost the fun though. I always enjoyed the beginning the most, and the middle & end game the least. When the alien ships became quite big, and very frequent I sort of got tired of the endless combat & micromanagement. I think that's a common problem with these kind of games which have 'games inside games'.

Hi

It's great that your making a game inspired with UFO and Master of Orion serial and these are my favorite games beside Battle Isle 1 and 2.Beside all of the things people already wrote which I also like in these games, I would like to add something. The atmosphere in the UFO Terror from the deep was for me one of the things that attracted me most. The music and spoky underwater atmosphere was great and added a high level of mystery like when you are reading a good SF book or watching a SF film and you can't wait to see what will happen next. New games lack this. Also I like the idea of being able to make damage to everything you see on the map.
I also like managment in these games and the most important thing the RESARCH of new technologies. The negative thing I would like to add is that Master of Orion 3 had, for me, much much worse battle then it was even in the first part of the game when you include everything.
Also I didn't like UFO Apocalypse not even close as much as Enemy Unknown and Terror from the deep.
The new idea for the game would be, beside standard equipement, waepons ... to make posibility for making custom weapons,equipement,vehicles from small parts ofcourse with some help about the rules of making these waepons described in the game(but not to much help). I would like to see weapon exploding in the hand of a solder because I experimented with the parts when I was making it. Or even better to make experimental weapon that is much better then the standard ones.

I wish you success in making the game that will have best parts of all of these games.

Psionics seems to have gone down hill in recent X-Com games. I really enjoyed mind controling aliens and making them drop their gear in X-Com 1. XD

In later games like X-Com: Apocalypse, psionics were virtually worthless (at least to me), as aliens were to hard to mind control, and that control was all to brief with few, if no lasting benefits. I think Psionics shouldn't neccessarily be nerf'd, but should be made more complex.

For instance, lets say you have a powerful psionic character, he mind controls an alien. Rather than having to constantly mind-control the alien every round within your line of sight, the alien could remain under your control every turn unless he successfully rolls his will willpower/psi over your soldiers. At which point he would break free and you'd have to find him again to re-establish control over him. To make it more balanced, the soldier would either be not be able to do anything while mind-controlling him (thus being completely vulnerable), or have X time units automatically deducted to maintain control over the alien.

You could also make it so that the soldier can only mind-control the alien for so long. Make it take few time units (or psi points) to actually mind control the alien, but have it Culmulatively drain X time units (or Psi points) each round. Eventually costing so many time/Psi units that the soldier has no choice but to relinquish control.