If we're purely talking about economy hiccups, the ones that really cheese me off (and IMO contribute to the problems you outline) are:
1. Not enough to spend money on - in real life we spend our money on shelter, food, clothing, and retirement savings. None of these apply in game. Sure, a character can *choose* to spend money for a meal here and there, and some places *might* charge a few silvers for the inn... but basically all of a character's money is spent on "adventuring gear". If you don't need to (or don't have the opportunity to) spend money on this gear (like most high level and mid level players who don't deal much in the production item economy anymore), you save it until you get a chance, or (in some chapters) you spend it on Plot items to feel good about buying a ship.
2. This is one of my personal pet peeves: people can make IG money by OOG means. Anyone, and I do mean anyone, can get basically infinite IG riches by bringing fudge, or root beer, or whatever in game and selling it for gold. I absolutely 100% hate that with a passion - it substantially devalues every single IG action that can be done to get IG money, and makes a character's IG actions to get said money nearly meaningless. Time and again I've seen the guy who works his butt off for a great IG con, or heist, or raid, or something, only to be *easily* outspent when trying to bid for the neat magic item by the guy who bought a case of bottled root beer and sold it for IG money. That quite frankly sucks, and my personal opinion is that no matter what else is done, the Alliance economy will *never* work because of this factor. I do realize though that my opinion on that is in the minority, and it's not something I often bring up or push for the reason that I don't expect it will change