I know this thread is a few months old now and it's probably too late, but i signed up here just to give my thoughts on this. I really, really don't like the sound of these changes, i think they're taking away what was great about the first game and the XCOM 1/EU theme.
The main issue i have is with the theme itself. The idea of a secret elite organization being created in order to prepare for a threat that seems incomprehensibly powerful was a significant part of what made those games appealing. It was the idea of your organization is the last line of defense with the rest of the world failing to adequately deal with the problem, as for them it was a sudden unexpected event, so your task to raise an army specifically equipped to fight the aliens all the while trying to hold back the escalating invasion however you can felt like the stakes were very high, the setting revolving around that was a substantial factor in what made the game what it was. It was a sense of basically "Earth's already lost, it's a race to buy more time until you can find a way to defeat before it's too late". Xenonauts having that idea set within the Cold War made it even more interesting, as it made it more like the Cold War itself was a cover in some ways and the real threat was the impending alien invasion.
Changing all that to two secret groups fighting each other feels far too small in comparison and entirely changes the most defining aspect of the game in a negative way, to me. It becomes less "Earth VS Aliens" and more just one organization who don't like aliens vs one group that does like aliens (because they are aliens). In combination the idea of the Aliens not having the power to really do much damage to earth makes them seem like a lot less of a threat, if it's a situation where you could basically replace those aliens with humans and it still feels like it could be a plausible scenario, i don't think that's a good fit for what should be an alien invasion game. It overall feels somewhat similar to the plot of XCOM 2 at a glance, but it isn't really - XCOM 2 was more about you trying to undermine the aliens from the shadows and take back control over the planet as a whole, that was a plot with a bit more weight to it than what appears to be 2 secret groups both fighting over the earth in secret.
Basically, the idea seems to take away the whole "us VS them" theme and replace it with a much less high stakes, more limited plot. The game should be about fighting off a full-scale alien invasion (or in the case of XCOM 2 doing so after they've already won) and having to build up an organization specifically to do that and buy more time until you can win. Going from "There's no one capable of doing this except us" to just "No one knows except us/we can't trust anyone" substantially changes the feel of the game from an Alien invasion simulation to a more mundane spy game with an alien theme slapped ontop. It feels like it's not using the idea of an alien invasion to the best of its ability as it's something that could be done with more typical human characters instead of the aliens and it wouldn't be that much different.
Alongside that the idea of the enemies mostly being alien-controlled humans sounds quite disappointing. Having a variety of different alien species as enemies along with the different technology and ways of fighting them was part of what made the previous games great. Changing that to mostly humans takes away from by making it feel too similar to your own character, it doesn't lend itself to a "Humanity VS alien invaders" theme as much. That feels like something that should be a secondary mission type, not the focus of the game
What i would have liked to have seen would have been a combination of the two things - an alien invasion alongside more secretive spy-like stuff. You could have something like a full-scale invasion as in Xenonauts 1, but that is just a cover for their real intentions. They're invading the planet in order to cause chaos and sow disruption, leaving things open for them to infiltrate and take control themselves as they're secretly searching for something, gathering information behind everyones backs as they're too distracted by the more obvious, visible invasion going on, with the end goal being they find what they're after and then wipe out the planet. So the game would have both the usual style of gameplay, as well as something more along the lines of this new theme and mission style; you're on one hand trying to combat the aliens to help buy time, while also secretly engaging the aliens in the shadows to stop them finding what they're after with you being the only one to know their real intentions. They could be after something like an Ancient artifact that organizations around the world have vague knowledge about, so they're infiltrating them to find clues. Just a quick example but i feel something like that would be a far more interesting take on this sort of idea, at the moment it feels like it's just half a game, in a way.
Basically, i feel like with this theme, the gameplay change and the removal of stuff like air combat and vehicles that i read about, it's moving away from what the game should be about.
