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.
From what I recently read in the Splash Cover Game Informer for ME the are going to keep the current system with tweeks. They said that the destruction of the Normandy and Shepard were a reason to make those changes and they don't want to go with a complete overall ut they did say they will be modifying this system to responds to the lack of role playing aspects that were the major criticism of ME2. Sounds like good news.
The say they are also modifying the mineral scanning
And not to expect the Mako hammerhead to make a full time comeback as it was in ME1.
If you ask me Mineral scanning should be pretty darn perilous with Reaper running around.