In regards to 'what I wanted', I suppose most of them should be considered in the context of ME1 carryovers.
First and foremost, I really wanted the side-mission carryover references to work: the hidden files show they were intended to, but it was sad that they didn't.
In general, I wanted more 'enivronmental consequences', good and bad, for both sides.
I wanted, was expecting, the Batarian Rebellions referred to by Balak to matter. We get a few side missions, but nothing else. Balak being let go should have meant something: another attack here, a minor atrocity there, nothing necessarily on the scale of Terra Nova, but he raised a plot point and it should have carried over here.
In the carry-over from Feros, I was actually hoping for the researcher's daughter, Elizabeth, to make an appearance. She would have been a good counterpoint to Shiala, and for similar reasons ('I made a mistake to them, I should fix it'), and even could also apply to some hero-admiration towards Shepard.
From Noveria, seeing Lorik Quin again would have been great: that Turian was the best Turian npc in the game.
More relevantly, however, some sort of 'thank you for saving us from the Rachni' stand-in for the Rachni ambassador would have worked well as a balance. Maybe a Noveria suit (Lorik himself?) who passes on the Executive Board's gratitude for Shepard resolving the matter in a good way, and with a promise of future reciprocacity and support in the future as a quid-pro-quo. Or, if this counters the Paragon asset of having the Rachni armies later, and Noveria really couldn't/shouldn't provide a similar role, the Noveria executives could immediately give this Shepard a significant number of credits/resources/'developmental tech upgrades' immediately now, and promise/imply future offerings in the future. That would balance superior strategic gains later with smaller tactical gains now.
Moving on to characters, I had hoped/expected to meet the Virmire Sacrifice's important relation at some point, possibly the Citadel. Either Sarah Williams, Ashley's sister, or Rhana, Kaiden's old flame. Possibly there to take part in/watch a memorial ceremony of some sort for the Virmire dier, they could be conflicted or even confrontational towards Shepard for letting the Virmire Dier, well, die. You could, would, talk them down soon enough, but it would be another sort of reminder about how your choices in ME1 shaped things for other people, not just yourself, and possibly in a gut-shot way. Eg, Sarah Williams might demand to know if you let Ashley die because of who her Grandfather was, and reveal she's going to join the Alliance like her sister did. Rhana... might have a more serious discussion on Kaiden's passion versus composure, and could be on her way to being an instructor at the Ascension Project.
I've always suspected/expected the Virmire Survivor to become a Spectre. Expected Garrus to become a Spectre as well, like he said he was thinking about: his Recruitment Mission could have been reframed as 'Spectre operation gone bad' or somesuch, or maybe he was on a mission, and went rogue to help the people.
Point is, him quitting the Spectres attempt caught me by surprise.
I always wanted to hear more about that Alliance lieutenant you save from being overrun by Rachni. That was a surprisingly unique and fun extra mission back in ME1.
Similarly, I sort of hoped that if you did/didn't do the Wrex's Armor sidequest, you could get a news report about Krogan artifacts or something.
Final, big thing: I think a lot of humans (or at least Alliance/Cerberus types) should have been angry at Shepard for sacrificing so many human lives and strength to save the Council, just as many aliens (but not all) dislike the Humans in the opposite scenario. Yes, Humanity got it's Council Seat, but the game continually portrays the Council as obstructing or refusing to help the Alliance in it's concerns, same as before, while the Alliance lost such strength after saving the Council (really should have done far more than eight cruisers) that it still can't protect itself.
A lot of humans should have been angry: 'Thanks, Shepard, you saving the Council that never did anything for us when we needed help gave us a pretty Title that doesn't change that they still don't do anything for us, while you got so many good humans killed that the Alliance can't even help itself now!'
And, to inverse the dichtomy even more, Shepard's reception by Cerberus overall could have been far more chilly, with only the Illusive Man really suporting Shepard's unique role as an asset to Humanity. Whereas a 'concentrate on Sovereign' Shepard is warmly received as 'willing to do whatever it takes' and 'remembering his species' and gets the overall warm welcome, a 'Save the Council' Shepard is maligned as taking needless galactic risks, as a xenophile (if romanced Liara)/species traitor, and the whole of the Cerberus is no happier working with Shepard than Shepard may be working with Cerberus. The only person truly supportive of Shepard is The Illusive Man himself, while everyone else (besides Jacob) is working on/with/for Shepard because the Illusive Man told them to.
(And, as a added layer of effect: while the Cerberus personnel might be professional and courteous to Shepard's face when he's talking to them, the full extent of the tone would be conveyed in the gossip you can 'overhear'.)
I think it would have posed a good Paragon/Renegade balance in the galactic structure overall. You can be on good terms with the galaxy as a whole, but not be appreciated or liked by the human establishment. Or you can have the inverse, loved/heralded by your species, but distrusted and disliked by the Council Races. A far better balance than 'loved by Humanity alone or loved by everyone.'