My greatest gripe at this point is initial unit generation. Every time I start a new run, it ends up that the first contract or two is brutally hard due to personnel issues. I do know its been mentioned that the Company Generator is outdated and is known to need work, but I feel like it needs that TLC sooner rather than later.
Right now a new run necessitates a chunk of initial downtime just to hire enough personnel to reach basic functionality. You're direly understaffed with support crew (both techs and admin) and while there's enough backup pilots to account for injuries, I find that generally by the second month of a campaign you're going to be running nothing but 6+/6+ pilots as the advanced medical rules are brutal. The extreme low skill level of techs also means that even basic repairs or maintenance can be nearly impossible.
This difficulty evens out after you've had a contract or two to skill up/wash out the weakest links and hire some better people, but it makes the starting scenario quite painful.