Not that I feel I have any right to dictate the game's design, but I'd like to make a few suggestions based on my experience with 0.9.0 so far:
1. The ATV and fuses are too expensive. The ATV is pretty crap compared to 0.8.2's ATV--it seems slower to me, you can't go up steep slopes, the light is worse, and you have a tax in the form of a car battery, which must be swapped out at the cost of 150 points now and then. The cost of batteries on top of fuel on top of upgrades is absurd, and that's if you can even bring yourself to use the damn thing instead of just sprinting everywhere with the hiking boots. (And if you break it, you have to fix it with a toolbox! Run out of those and you're spending even more points on the ATV. Worse yet, you might lose a tire and have to buy a new one.)
+ Fuses blow really fast for how much they cost. 100 points for something that might even not last the day is criminal.
2. Dr. Bao's daily tasks are too demanding early on. I find myself having to babysit signals and panic to complete daily tasks in the first few days. Sometimes I simply don't get enough time to complete a daily task--Dr. Bao asked for too many drives and my download speed is too slow. I'd upgrade it if I had points, but I need to earn points before I can use them.
3. Coordinate towers break down too often. Wouldn't be so bad if fuses weren't so expensive, but a single coordinate tower going down can bottleneck your entire operation. Maybe add a permanent upgrade to make the towers last longer?
4. The tutorial does not adequately teach players how the game works. I can't even remember if it mentions coordinate towers or the radio tower, but I know for a fact it doesn't demonstrate them. You also don't get to learn how getting reports works first-hand, you just have to remember what the wall of text said to you an hour or so later and figure it out on the spot. I would rather have a shorter tutorial that walks the player through each of the game's main activities (capturing and processing signals, getting reports, fixing transformers, fixing coordinate towers, fixing the radio tower, and sending in the daily task items).
My suggestion: the tutorial should just take place in the normal map without events. Without big walls of text, guide the player through all of the things they need to know. Have a transformer break down when it's time for the player to learn how to fix one, etc.
5. Not related to game design, but can something be done about the game's performance? I've got a mid-range rig and I'm not trying to play on max settings. This works fine (60 FPS or very nearly 60), except when I'm in the base, where the framerate dips sometimes as low as 25 FPS.
Besides all of this, I've mostly been enjoying the update and I think a lot of the changes are fun and sensible.