First of all, amazing game.  I haven't wanted to play a game a second time right away like this since Resident Evil 4.  But anyway, about the topic...
 
1)  Does it annoy anyone else that skipping dialogue and selecting dialogue are both assigned to SPACEBAR?  Not so much an issue on the first run when you want to hear all the dialogue, but I know on my second run I'll inevitably pick the wrong dialogue because of it.  It's really the main reason I feel the need to quick save so often.  It's not that big of a deal, I know.  The fact that it seems so easily fixable just gets on my nerves.
 
2)  Scanning planets.  Mostly optional, but I didn't know that as I was playing, so I ended wasting a lot of time building up a stockpile of minerals that, as it turns out, aren't even necessary.  Maybe it's because as an engineer research costs less, but man, I literally wasted hours scanning planets for no benefit.  Also it would be nice if a narrated description of the planet played while you scan.  
 
3)  Glitches.  I had to restart a mission once because I got stuck floating over an object.  For the sidequest with the 2 missiles, the journal says I made the opposite choice of what I actually selected.  And the sidequest that involves delivering a package for the Salarian, Ish, the journal still lists it as active even though I finished it.

1) Yep, ME1 already had the same issue when I remember correctly. Using the mouse button as workaround instead should help. Speaking of keybindings, one annoying thing is that the GUI is only in small parts keyboard controllable and in those parts where it is, it works *only* with the cursor keys, not with WASD. Would have prefered a fully keyboard controlable GUI, as that would have speed some things up a little.
 
2) Scanning felt rather pointless, I preferred driving the Mako around, might not have been perfect, but at least it was fun to drive, scanning in ME2, not so much. Would have prefered some more interesting drivable planets over no drivable planets.
 
3) The credit chit quest on the citadel seems glitches for me (or maybe I just haven't figured out the solution?), journal says I have the chit and now need to talk to the officer, but officer only responds with the same text as before. (Edit: not a glitch, quest was solvable normally, it was just the journal entry that was extremely confusing)

No Glitches for me so far! just got to the second disc on 360, which is just as you get the second round of dossiers.
 
scanning is stupid boring you're right, i'm not an engineer however so maybe it's still worthwhile for me. I have a hell of a lot of the second mineral on the spike chart, hardly any element zero though, and platinum goes as soon as i get it. All they really had to do was speed the process up, or make the probes have a wider area of effect. Or got rid of probes altogether and just had you roll over stuff to pick it up? either way you'd think mineral hunting would be a job for the CREW >:( 
 
they could have just done an assassins creed 2 and have you invest in a certain area of your ship, which over time earnt you your money back through automatic mining. Active Planet exploration could just have been limited to repsonding to distress calls, which they could have made more common, even at a cost of having more generic planets if would have been nice to actually DO something during the grinding.