There's one big problem I've noticed: the game has an inverse difficulty curve. The start is daunting because everything is a mess and all your instruments suck to use, it's only after you have better upgrades/modules/equipment you can relax a bit.
The new server repair minigames are kinda frustrating. They also become redundant as soon as you get a Kerfur.
The ATV battery was an annoyance until I got an alternator, at which point it become a non-issue to the point of not really being a feature.
Triangulating signals was awful at first but is now trivial. The towers are still a nuisance to maintain though.
Restarting transformers is a huge pain, but with max upgrades they need almost no maintenence.
There was so much base cleaning to do that after removing the rubbish, I just used the reset feature to remove grime/stains. I tried repairing the cracks myself, but it was so laborious that I removed those too. I did enjoy cleaning the base in 0.8.2, but it's too much work now.
I think it would benefit the game if some mechanics were introduced gradually. Maybe something like for the first week you are only expected to get signals, then second week they want tapes, third week they want hash codes.
Because I don't want this to sound overly negative I will say that the new ATV is a huge improvement, it handles better and the modules are really nice. The mounted radio has seen a lot of use from me.