The first big thing in my head is that cutscenes can break immersion for me if I have a Shepard with any biotic abilities at all. In quite a few cutscenes, it would make perfect sense for Shep to use biotics (chasing people, to cushion a fall) and yet s/he never does. So yeah, it'd make most sense if Shep wasn't a biotic.
Also (because I'm INCREDIBLY anal) I have a few personal RP do's and don'ts for ME1:
- DO go *on foot* to see the council for the first time. Ashley has a line about 'that weird bug thing' on the Presidium in front of the elevator to the council chambers. She does not appear to know what it is. Yet upstairs she will point out Chorban 'scanning that Keeper'. If you go to the council via rapid transit and miss Ashley's first line, she will say it later, and it'll sound weird and the world will implode.
- DO start the Asari consort mission and the Rita's Sister quest ASAP. I do all this to avoid visiting Chora's Den after you've totally torn up the place to get to Fist, only to return a few hours (?) later to see the place pristine and exactly the way it was before.
- DON'T go to see Barla Von. I think Garrus and Wrex's recruitment plays out more logically if you go to see Harkin, then help Garrus in the med bay, then fetch Wrex, then go to see Fist. If you go through Barla Von it's hard to RP not just getting Wrex and then going straight to Fist without getting Garrus at all.
- DO start as few side missions as possible before becoming a spectre. Some missions are fine, but others (such as Emily Wong's, and Scanning the Keepers) make much more sense that people need your help because you are a Spectre. If you get the missions before, they might say it's because you're an amazing war hero, which works less well, I think.
- Plot-wise it makes sense that you'd bring Wrex with you kill Fist, but then again, the squad you take with you to Fist's hideout is the squad you have with you when you present Tali's evidence to Udina. And it is jarring that Udina is surprised to see Tali with you ("Who's this? A Quarian?") when there's a hulking great Krogan standing next to her as well. Or even Garrus, really. The dialogue flows naturally if you have Ashley and Kaidan with you, but then you'd have to think of a reason you didn't bring Wrex to kill Fist. Either way, something is going to jar a little, annoyingly.
So, Mission Recap for your first arrival on the Citadel:
- Start at human embassy
- See Elcor diplomat for Consort mission.
- See Sha-ira.
- Go to council chambers (on foot for Ashley's 'bug thing' line. You can then ask Avina for some Keeper exposition).
- Go to Flux (probably the hardest thing to explain, RP-wise. You could imagine you got lost, or went to the wrong club in search of Harkin, or desperately need a drink, or whatever). Talk to Rita to get her quest.
- Go to Chora's Den. See Wrex's run-in with the bouncer. Then talk to Jenna, Harkin and General Septimus all in one go.
- Go to med clinic to get Garrus.
- Go get Wrex.
- Go get Fist (with or without Wrex - up to you).
You are now a Spectre. This means it makes a lot more sense for everyone to be asking you for help since you are a law unto yourself. Also, Garrus and Wrex are recruited in a plot-logical way. And you don't have to go to Chora's Den again (there's no Keeper in there or anything) and can imagine it lying in smoldering ruins for the rest of the game (or for Fist's replacement to spend ages doing it up only for it to get trashed by Geth/Sovereign for extra lolz).
And yes, I have spent way too much time thinking about this. But it irks me that the first citadel encounter can be quite a plot mess.
As a passing thought, unless you're in a meta-gaming hurry to get Liara, I think the most logical mission order is Feros (Geth sighting and colony gone dark? Pretty urgent) - Therum (if you want Liara first you could imagine you're trying to get the drop on Saren rather than following in his footsteps, but otherwise Feros sounds more urgent) - Virmire - Noveria (if you do this earlier than last it feels odd that Saren hasn't already gone to Ilos waaaay before).
And as a love interest, Liara feels pretty canon - salvaging your body in the hope Cerberus can bring you back, her 'final vision' she gives you in ME3 before the final assault... Works fine if you're just friends, but I think works even better as romance. Just saying'...
Hope that helps.