Two things I ran in to early on in RT was that players can essentially acquire the best everything (more or less) and that the ability upgrades were a little too low, in my opinion, at only +5.
So as a house rule I implemented that excessive requisition, going on a shopping, spree will eventually lower their profit factor as well as steadily increasing the checks due to merchant running out of stock (they need to supply other people after all).
As for the ability upgrades I increased the first two upgrades to +10 and kept the last two at +5 with no further changes. I agree with my players personally when they say "I want to be able to hit stuff when I attack".
Anyone agree with these or have better solutions? I'm always looking to improve my style.