Some changes to hacking and lockpicking could save a lot of unnecessary clicks and time. The main one being why can't you simply right click a locked container/shaft cover and get a hack/pick option? Having to open the inventory, find the tool, right click it, and then click the target seems unnecessary. Even moreso for the omnitool which requires an additional click, even if there is some reason for having to select tools, the omnitool could just be context sensitive and lock/unlock hatches based on their current state. We already have the relatively long countdown for these actions so the additional overhead of UI manipulation seems unneeded.
An additional big one would be an option to right click in-combat and get an action list (or something with a similar effect), doors/bodies can be a huge pain in the ass in combat when you want to move onto a body, or are trying to target something behind a door, either requiring pixel hunting for a spot where you can manage to click the floor/target, or if you're unlucky accidentally looting a corpse/interracting with a door and potentially having to reload because it messed up the fight. If "Action List" doesn't quite get the point across, I imagine a situation where a target is behind a door, so you can just right click their outline and get a small dropdown with the options "Attack $target" and "Close Door".