I've had a chance to load and play the 2.0 version. So far, I'm loving the weapons upgrade for the ballistic weapons. Being able to upgrade the laser weapons to have batteries has been great as well. The costs are a bit high, but I'm working with it.
The armor system upgrades have been awesome for me. I love the drop down for the modules, although I wish the menu didn't hide the popup information about the modules. I saw you were saying the modules would get artwork if you moved forward with this system, it would be cool so see that.
My only other functional critism would be on having duplicate engineering projects for the same upgrades involving the new alloys for aircraft and armor. They're the same thing according to the lore on the upgrades. So I'm curious, why're we having to pay for this one twice?
For the Cleaners maybe having more cells with smaller amounts of research earnable or having a cap based on how many cells you have cleared from the map. I tend to just do one of the 2 cells to get the research percentage started and let the time run out while dealing with the aliens to find their base. Then when I'm done with whatever alien missions I have queued I knock out the last cell and the main base back to back. The group just kind of feels like an afterthought to me.
Hope this helps you guys.