I would change a lot of things.
The necessity of points in technical abilities in order to decrypt and open objects would be gone. It wasn´t fun. It was restrictive and offered no real advantage.
There would be possible landing points marked for the mako in each planet.
No need for two runs in order to reach level 60.
Items would jump-level as you researched new tech.
There would be heavy weapons designed to fight larger enemies on foot.
Tali and Garrus would be possible love-interests. And since he was revealed as gay in ME3, I have no objections to Kaidan being gay from the start as well. Ashley would remain strictly hetero.
Running and taking cover would work as in ME3. Jumping would be added. Or improved, since you can actually go over some items.
The dlcs would become possible to play after the main game is over, a la ME2. There could be a handful of new adventures with the original normandy in the months prior to its destruction.
Assuming he was able to survive Virmire, the salarian capitain could become a later squadmate.
As originally intended (one old trailer displays it) it would be possible to take possession of a squad-mate and manually use him or her in battle while shepard becomes cpu-controlled.
The AI of the squad-mates would be better. More than often they fail to obey me and behave in strange manners.