Gents,
I know you're writing a game on a shoestring with volunteer work, so obviously take what I write with a grain of salt. I really do appreciate that you guys are working in a genera in which none of the big-name gaming houses are even thinking of working in, and which Bohemia Interactive as a small-time outfit got royally screwed by it's american publisher for writing in with Afterlight.
Having said all this, I now have some design suggestions to heap onto what is probably a huge list of things you'd live to implement. Maybe some of mine will rise to the top.
1) Mission pacing: in my 55 hours I completed on the order of 350 missions, and was pretty (yawn) bored with them by the end of it. It's not that there weren't enough maps or variations of maps, although I did start to get tired of them, it's that you guys put me through 350 missions in 9 game months, such that I was even bored playing brand-new maps that occurred late in the game, like the subway map. You might counter that I had the option to automission some of them. I didn't, actually, because in my version (3.2.1) the only mission autmission would ever win was a base defense mission. It would lose every other mission with no Phalanx casualties no matter what the kit or experience of my troops.
Honestly, tactical missions began feeling like punishment, such that I disarmed all my SAM sites and let the UFOs come straight to my bases so as to be able to autoresolve base attacks rather than fly fighter and scout crashsite missions all day.
My suggestion is that you need to readjust the pace of the tactical game versus the strategic game. Stale maps take on new flavor when you've got new tech to employ on those maps, but if your tech progresses too slowly, than you'll have to do 25 missions before the next new tech...
2) By the end of the 9th month, I had almost 30 recruits sitting around with no job. I would have loved to have been able to employ them in a "regional garrison" that did for ground missions what the SAM sites did for air combat: autoresolve them. Imagine: the garrison could autoresolve any crash missions within it's range ring. And, from time to time, the aliens might attack a garrison directly like they do bases, leading to a new mission variation.
3) If you want to keep the grand scale and onslaught feel of "alien invasion" with upwards of 1.5 missions a day (which is what I was hitting at the end) I do suggest you allow at least partial experience on troops for automission successes. It only makes sense: if the commander is risking an asset (soldiers) then it would be good to have some improvement in those assets with success.
4) Add some single-stroke commands. Consider a task which I had to do routinely: have a troop draw a medkit from a holster, apply it to his buddy, and put it away. This required click (open inventory) -click drag (move from holster to left hand) -click (close inventory) -click click or xx (cycle off reaction fire) -click click (open device menu and select heal) - click (select heal target) -click (open inventory) - click drag (return medikit to holster) -click (close inventory). Count them all up and that's 13 mouse commands to do one thing that needs doing over and over. Ouch!
Diablo, for example, allows the player to switch from one equipment set to another with a single stroke. Implementing something like that (but which deducted the TU's required, obviously) would help reduce all the crazy-making clicking your legacy interface from UFO:ET or XCOM creates.
5) Create some way for the player to choose which forces in a bases will be employed first to respond to a base attack. For example, my firebird troops normally carry laser weapons as their primaries, great for ranged fights, but less than ideal for base defence. But when I started keeping close combat and heavy troops in the base for a dedicated base defence, my firebird troops would be employed mostly anyway when the base was attacked. I wish I could have designated those 8 cc and heavy troops "garrison defence" so that my firebirds could have stayed well rested and ready.
6) Not sure of the role of the plasma blade. Seems to just be a way to create player casualties. I never encountered an enemy armored vehicle or drone, so I wound up just using them for my CC guys as an "oh shit" weapon. But that "throw" function? I've handled shape charges IRL as a military engineer and trust me, you aren't going to "throw" a bell shaped cone and have it stick to anything, much less even land cone-face on target.
7) A way to show rank on the character screen during battle. This will allow the commander to choose from amongst the troops who to risk (or who to give the skill-improving gimme-shot).
Another click-reducer: eliminate the movement interrupt for enemy spotting. For example, if I spend 25 seconds working out where I want my troop to move to, then click that square, I don't want to have to re-work the movement order 3x times if he spots 3x enemies on the move. Something like a "continue order" option would be great rather than hunting out the same square on the ground and clicking it 3 more times.
9) Consider some "intermediate techs". As it stands your tech tree is kind of bare, and the only way to improve your weapons is to jump to a whole new tech. A way to give the player to have something to research, as well as to keep different weapons types relevant as the game progresses, would be to have intermediate techs. Here are some suggestions:
"Improved DF cartridge." Upgrades the DF cartridge to hold more energy, allowing more laser shots. Or, if you wanted to avoid having to track multiple DF cartridge types, you could do "efficient lasers" that keeps the DF cartridge the same but allows more shots. Or you could even combine the two.
"Improved EM weapons" could increase the range or rate of fire of an EM rifle or decrease the cost of the magazines.
"Blast ammo": blast slugs for MG.
"Napalm shot": fire slugs for shotguns.
10) Consider battlescape saves. I realize this risks having some players turn the game into a save-reload fest. But while you're in beta-testing, allowing battlescape saves would give you some distinct advantages. It would allow players to reproduce bugs more efficiently, rather than forcing them to play and attempt to crash another mission to reproduce the bug. It would keep them from getting as frustrated by the bugs, so they didn't quit before they supplied you with good data and go back to the world and give you bad press.
I don't want all this to sound like criticism but suggestions. I know you have full plates for a non-profit project so all this is pie-in-the-sky. My last computer programming experience was intermediate pascal in college (1988) so I'm probably not going to be able to program to back up your project. But I'm available to do plot and research proposal-completion text-writing.