Intended Improvements:
Full 3D - 3D wouldn't be terrible, but I agree with the other posters that the game does have it's own retro charm now with its current style. Maybe have 3D in certain sections of the game, but I don't believe that the game would be benefited from everything being 3D.
Aliens - Since this is a remake, not a sequel or a large update, you have about the same options. You already have your basic aliens, but as a weird idea, maybe have multiple factions of aliens. I wouldn't know how to implement it but of my two ideas...
1) Maybe this could effect the previous ideas of a cold war, but maybe there's a kind of same idea with the aliens and are using Earth as a battlefield for their war, instead of their planets. Winning would include destroying one of their planet or home or something. Maybe you could choose a side, one being more powerful but slaving and will take a large portion of humans for slaves, or the other one being weaker but ensures freedom within a republic.
2) You could choose which enemies you fight, in faction oriented menu at the begging. Maybe you fight slavers, or crazy gene manipulating enemies, or robots, a slightly higher technology human-like race, or your default slave confederacy of aliens.
Research / Development - For research, I think enough has been said. Make a tree, not a log. For development I'd expect something more modifiable. Such as being able to add things to weapons or armor to change an attribute of them, rather than having multiple suits of armor that are kind of the same but keep costing more or less. I'll just use Wolf as an example, you have wolf armor and the flying wolf armor. They cost different things even though they kind of match out at usefulness, based on situation. With weapons, you could have easily assembled mods, like a grenade launcher or a better sight.
Destructible UFOs - That's a good idea, but it may be difficult when there's something needed in a UFO, I don't know what, and you threw a grenade to catch an alien, suddenly you have to attack another battleship. So +1 overall
Vertical Terrain - I'll play devil's advocate here. Anybody else remember having problems in the original x com games, whenever bullets/harpoons were just too low or high to hit an alien? Or when the mountain or hill cause your pullet to just barely not nick the feet on an alien? My real opinion is on board for verticality, but that's not to say I had no trouble getting used to it.
XCOM Cover System - Which one? I'm not entirely clear on whether you mean the originals or the remakes. If the originals, I don't see a difference. The remakes, I'd rather this depend on the graphical style. I would prefer some minor changes in the cover system, more percentages and more intuitive numbers to where they can and can't be hit.
UI - If it is a mess, it's a hot mess. I didn't have many problems with it, not nearly enough for myself to mind anything. It was good.
Air Combat - Paratroopers? Possibly dropping soldiers onto/into a UFO and having to fight against them literally pushing you out. This could be achieved with the verticallity.
Tutorial - If everything comes true and good, a tutorial will be needed. At the very least, more tooltips.
Two questions - one, would you buy an improved version of Xenonauts again if we made it?
Yes, maybe. Sale, yes, anytime, but please release it at a good time. Not right next to a big seller or something like that.
Secondly, what annoyed you about the first game and what do you think we should improve?
Some buttons like the Build New Base button were too small.
I loved the shield class but didn't figure out how until a while in.
The difficulty ramp is fine, but not when you can't see it coming.
More enemies. I don't want to you to blatantly rip off X-com: Enemy Within, but I wouldn't mind a genetically modified human enemy that worships the aliens. Or then genetically modifying your own soldiers.
I think the prospect of robots or cyborgs could help improve the game, but not actually implementing them. Like researching enemy mechanicals can give you a better health kit or make healing/reviving easier. i don't know but robots/cyborgs would be a good idea, if not a mechanic or concept.
Money issues only a few months, or two months in.
Shooting percentages. It seems like getting blocked by an item and shooting an enemy had two different total percentages and combining them would be a good idea.
