Personally, I would kind of like to see them go to an upgrade system like Resident Evil 4. That is, you upgrade the various statistics of a weapon with monies.
I would also like to see them eject the entire "find an upgrade" system they had in ME2. Find a weapon/armor (blueprint), sure. But I'm not scouring the known universe to find a 10% increase that my brilliant scientist should have been able to research if I'd have given him a little more coffee.