So, what are the features you'd really like to see in NuNuCom? I think that while the streamlining of the combat in NuCom actually made it more tactical and interesting, the whole strategic part of the game (air game, base management) was lacking, so I really hope we see an improvement there.
Some of the things I'd like to see in a sequel.
Pilots for your craft that can gain experience. Possible upgrades for interceptor pilots include, higher accuracy, chance to hit a weak spot for massive damage, longer time before UFO escapes, higher chance to dodge enemy fire, increase in fire rate, increased bail-out chance. Possible upgrades for Skyranger pilots include, aerial recon(more area explored around skyranger at start of mission), improved deployment area, fast takeoff(for a turn or two longer mission timer), faster strategic map speed, local radar(to give a turns notice of incoming enemy reinforcements, when appropriate)
When levelling troops, the option to pick an earlier upgrade if none of those on your current level are of interest.
Multiple bases. Even if secondary bases are only locations for Interceptors and Skyranger teams to base out of and research/manufacture remains limited to the main facility.
Training facilities. Perhaps limited in how far they can train to, but allows for not sending rookies into the fight unless necessary.
More base defence missions. Ideally ones that are effected by how you have actually laid out your base.
More base attack missions. Possibly as part of a way to liberate countries that have fallen to the alien.
Ability to target a wall/door/piece of cover directly. When stray shots can bring down entire walls, the idea that you are trapped in an alley because there is no door should be ludicrous.
Squad scale EMP/anti-robotic weapons. It fine starting out without these, but by the point that you know there are going to be robotic forces on every mission these really should start being developed and carried.
More variety in terrain of maps. Deserts, Tundra, Ice fields/Glaciers, Fields, Farms, Forests, Coastal, Towns & Cities(that actually vary in appearance so it's not all small-town America).
Map randomisation. Even if it is limited to pre-built chunks of 8x8 or 16x16 that are assembled and randomly rotated to form the map.
Modability. XCOM was artificially made harder to mod, for little good reason. The only real requirement would be for clients to do a matching crc check of their data when jumping into a match and possibly have random matchmaking limited to an unmodified set of data.