Hi!
(1) When you focus your production on a given category it doesn't update the research time-to-discover value.
Flaw.
(2) If you fly a troop ship near a starbase the civilization owning that starbase decides to go to war with you.
Feature for planets, flaw for starbases.
(3) If I fly a freighter to a planet and I already have my limit of trade routes the freighter will sometimes just disappear. I mean really. Why does it completely disappear?
Never had that one. Likely a flaw.
(4) When my cash hits greater than 10,000 bc my trade income goes all to hell (i.e. lower). I like to keep a warchest in case a civ declares war or a bad Galactic Event occurs. What was the thought process behind a 10k bc limit anyway?
Design feature. If it annoys you, just wait until you hit 20k treasury and got additional 20% penality to your econ ability.
BTW trade in GalCiv-2 isn't the main source of income as was in GalCiv-1. Here it gives 2k-3k money (usually negligible), and bonus to relations (main issue).
BR, Iztok