If we get some kind of stronghold in MEA and they don't do ME2 style planet scanning (most boring meta-game ever) then it could work.
For instance, you have an R&D team at your stronghold and they collect limited amounts of local resources to experiment with as you're going about your missions. When they make a breakthrough, for instance something that improves your shields, or maybe armour on the Mako, then they can ask you to keep a lookout for those types of resources as you're going about your missions (akin to ME1).
You'd simply need to secure the locations of those resources and your research team could then go about mass producing the gear... this could upgrade the grunts protecting your stronghold, make mods that improve your weapons or armour (or unlock new weapons/armour) or upgrade the Mako or stronghold itself. I'm sure there was something similar in DA:O or Pillars of Eternity.... take that idea and space-ify it.
After all, we are supposed to be pioneers in a new galaxy, any resources required to make, maintain or improve equipment would need to be sourced locally - through trade, gathering or otherwise. Just don't make it a tedious grind that you have to go out of your way for or have the player-character needing to try and cobble the gear together themselves - "Damnit Jim, I'm a space ninja not a wrench jockey!"