My thoughts on some of the listed points as well as some other things, from the perspective of a non hardcore player who liked the XCOM remake but never played the original.
Full 3D: I'm ambivalent about this...3D and 2D isometric are both good when done right. I do agree that ditching the paperdolls is a good idea, and whichever path you take please do try to make the characters less cartoonish. Or make everything more cartoonish if that's the style you're going for...as it is now the characters and environment just seem really disjointed.
Aliens: Mo aliens mo problems, I love it. Also like to see some alien species that do things that aren't tactically advantageous but just bizarre. Xenonauts does creepy way better than XCOM but it could really amp it up if the AI starts thinking outside the dimension.
Research/Development: I like this, especially if it means the chief engineer gets to throw some barbs of his own in reports. In general the R&D cycle should be more evenly paced, rather than research a whole bunch of nothing followed by a huge lump sum of awesome stuff late in the game.
XCOM Cover: Good idea, I like it. The current cover system is really unintuitive and gets in the way of tactical maneuvering.
Difficulty options: I want there to be more ways to tweak the difficulty level, as it is without mods I find easy to be far too easy and normal to be punishingly hard due to one of the three main game areas (tactical combat, air war, economics/region management) going badly off the rails. Ideally an adjustment scale for each one though checkboxes for select tweaks might also work.
Accessories: I want to equip my guys with accessories, e.g. reaper protection or extra sight range. Don't care whether this takes the form of a new slot or pistol plus offhand.
More stuff: More base buildings, weapon/armor options, aircraft, etc. would bring additional flexibility and depth. Both Xenonauts and XCOM are far too linear in this regard.
Side missions: I'd like to have a couple of small adventures in addition to the main war, for both passing the time and adding depth to the story. Perhaps add some hero units like XCOM's Triad guy, he was cool and added a lot of flavor plus a reason to care about at least one of your dudes.
Artifacts: A fun addition, perhaps as rewards for those side missions, would be unique items with powerful bonuses and perhaps also some disadvantages.
Additional base types: The strategic planetary defense simulator aka geoscape would feel a lot more strategic with new, minor base type such as SAM sites and local radar installations. And it's only fair that the aliens get a few of these, too.
