We've been flying Mesaba from LEX most of this year. The whole gestalt is a little funky, but as azj points out, the station is very short on staff. 3 or four of them will be manning the ticket counter, handling the bags, running the jetway, and acting as gate agents, and if there are 2 or 3 flights to deal with, I'm not surprised they get a bit distracted.
I have seen them board the whole plane at once - and don't approve, but it's not the norm. As for not processing upgrades, I haven't seen that. We've missed upgrading twice this year, but both times F was most definitely full.
What's been very tedious lately is not having the jetway to use, even when it's empty. I don't expect that's anything the local people have control over, however.
I am pretty worried about the whole Mesaba situation from a selfish point of view, though my worry is obviously nothing compared to the employees'. One of the FAs on a flight last week had on a "Save the Avros" button. Sure hope it can be done.
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