Regarding recruiting, take a lesson from their own Dragon Age team. You run in to potential teammates as you play through the plot, and you can recruit them if you want. You don't *need* to get them, though there's extra content if you do. Don't hinge progression on recruiting specific teammates, unless it's early and obvious (i.e. Alistair).
Give us some (significant) variation between weapons - Two or three different assault rifles, but with different function (One does more damage, but has a smaller clip and overheats faster, say). Keep research, but focus on upgrades that are modular - a pistol scope that increases accuracy, a longer shotgun barrel that focuses the spread (more damage if it hits, but a smaller area to scatter into a small hit), improved cooling, etc. Limit the upgrading, so I have to customize my weapons rather than it being a blanket "all my shotguns do more damage" type thing. Let me customize different teammates' weapons individually.
More conversation paths, more small details about the characters (even if it has fuck-all impact on anything) to give them depth, and let us pursue the RPG elements (not leveling, but interacting with the world through more than gun barrels) outside of the "safe" zones. I don't want to be able to talk to my companions in the middle of a firefight, but I do want to be able to talk to them when we're on the Citadel.
Bring the "you really could die here" danger out. Let the reapers strike a decisive and devastating blow halfway through, and let Shepard have to plan and execute a supremely dangerous strike behind enemy lines to open up the possibility of a counterstrike from the main Citadel fleets. The "you'll die if you mess up" danger in ME2 was barely brought up. Sure, overwhelming odds, but that's a day at the office. I want to launch a three-man invasion of an active reaper through a carefully-crafted fake torpedo, fight through waves upon waves of Geth, Collector and other, unknown, enemies to its main brain system, plant explosives, and run the fuck out to hitch a ride on a second escape-pod torpedo. I want to personally plant a nuke in an enemy base *without* a Salarian STG unit as backup, and then fight my way out instead of that being the end. I want real, pressing danger of failure, and I don't want failure to simply being a loading screen. Give me endings that I could bring on myself halfway through, that are a lot less victorious.
Oh, and *fuck* the mining bullshit. Replace mineral mining with stolen research data from enemy computers, or strange, undocumented astral phenomena that the onboard scientists can analyze to discover new technological possibilities. And don't have it be that godawful scanning-and-probe shit. In-mission, or as a component of a full side-quest.
More depth to the environment. Let me land on uncharted worlds and explore, find hidden bases for unconnected organizations - a drug depot for a cartel, a slave trading ring's storehouse - and give me stuff that *isn't* my fault. There should be a depth to the world that doesn't feel like everything is about me. Hell, give me a major plot mission that isn't actually related to the Reaper threat, but looks like it is.
^^^
My personal wishlist. But who am I kidding, I'll buy it without any of this. I just hope Bioware doesn't fuck it up.