The order I finally settled on is:
- From Ashes: post-Palaven, pre-Sur'kesh. Even tho I don't use him much on missions, I like getting Javik as soon as possible so I can start interacting with him. But I postpone it 'til after Palaven because evacuating the primarch feels like it's something that should be done immediately (and even then, Shepard is still too late).
- Citadel: the "Shore Leave" mission portion of it immediately after the coup. It's when it first becomes available, and the ship is right there anyway so it just seems to make narrative sense as a good time to stop there for a few days and have some repairs made. (The only downside to doing it here is that you don't have Tali yet, but unless your Shep is romancing her--which mine doesn't--then it's not really a big deal; YMMV.)
- Omega: Right after "Priority: Shore Leave". When Omega first came out, I didn't like it because it made no sense to me that Shepard would just leave the Normandy behind and put her/his ability to leave Omega completely at Aria's whim (suppose the fight to re-take it had gone on for months, and Aria refused to let Shep leave until it was over?). But by doing it right after the Shore Leave mission, I can believe that the Normandy is in drydock for a few days/couple of weeks, and Shepard figures it's as good a time as any to go help Aria. It's either that, or sit around the Citadel the whole time, watching biotiball with Steve & James and shooting holograms with Jack. Might as well go do something productive for the war effort.
- Leviathan: After Rannoch. As already mentioned, it just seems to make the most narrative sense to save it until after the first encounter with banshees at the A-Y monastery. And if you've already done the Shore Leave mission, then all the trips back to Bryson's Lab on the Citadel make a good excuse for doing all the various meet-ups with the crew in the apartment and on the Strip.
- Citadel: "The Party": After the end, with the pre-Cronos autosave point that the game returns you to. Make the party an epilogue, and treat it as a flashback (the stargazer's "One more story...") to some undetermined time after the Shore Leave mission. This lets you have everyone there, including Miranda, and not only does it not jar with the post-Thessia, pre-Cronos tone of the story at that point, but it fits perfectly as the final farewell it was written to be. I love having the very last moments be "It's been a good ride"; "The best", and watching Shep run off to join the rest of the team as the screen fades to black on the Normandy... *sniff*