Bounties not worth it in the middle of the game, but after i completed the story and got my Paragon, they became pretty good (not the hardest ones though...).
I started a colony and dropped to -80k per month. Get to 60k left on my account, and then i decided: "*** that ***, i wanna be rich" And started to hunt bounties. Got enough money to build everything you can build (including planetary shield) on a colony of size 4 before it hit size 5.
Just dont fight phase fleets. Pirates, ludd - doable with solo Odyssey. Conquest pack - doable with paragon and bunch of support. Few Onslaughts + few Legions - same, but slightly harder. And every of those will give you 200-350k. It is pretty ok, and you can do em faster because of... story reasons (spoilers).
Midgame is hard, i agree. Storms eat your supplies, crew eats salary. I had Legion + Apogee + 3 Champs + Fury, and it is not a setup that can do things. The game has no social lift. If you poor - you poor and it is pretty hard to get better (unless you just pick comission and buy any capitals you want, which is, well... good... but braindead feature). But when you good - it is easy almost as it was.