Jacob gets the Raiden/Luke Cage treatment. Drop the straight man act and give him some edge. In ME3, rather than run off like a coward and spend time hiding from the galaxy with a group of scientists who've recently gotten a conscience, he goes back to the Alliance with Shepard and back the Commander up. Give him and Kaidan some opportunity to show off their biotic power in a cutscene and make him more of a "take'-no-****" type of guy. As a bonus, he can space an enemy with Javik.
Kaidan, while a decent character, could be even better by not being such a nice guy in ME3. Make him battle hardened and follow up his post Sanctuary dialogue with some more of that fiery emotion.
Jack has a great arc, but it happens all too soon. Make the time leap between 2 and Arrival 6 months, make 3 about a year later. Then her ME3 appearance makes more sense. Also, being part of the Alliance, she should rejoin Normandy with Jacob.
Miranda get her business done with the aid of the Normandy. Make her supposed title ("2nd in command of Cerberus") mean something. She should point you toward Gellix, Sanctum, and Sanctuary. Keep the ice queen archetype.
Tali. Make her more mature. Its like she reverts to a child in the games. In ME1, she's young and unproven, slightly naiive, yet street smart. This Tali'Zora looks like a future admiral. In ME2, she shows some leadership and indepentant qualities during Freedom's Progress and upon her recuitment. Make her more confident and drop the drunken college girl garbage. I want to see her giving orders and mission suggestions in ME3, not being a follower and hollow leader.
Garrus is mostly fine, but I'd give a reason for dropping his lessons with Shepard during ME1. If more paragon, have him as a Spectre bent on taking down a merc band who drew the ire of the council. Renegade remains the same. Throw in a bit of his ME3 arc where he followed Shepard's lead in keeping knowledge of the reapers in the council's minds.
Kai Leng. Make him a tough bastard. That ice cold killer that Shepard can never shake. Make him a combination of Jack Krauser and Vamp. The boss' (TIM) REAL #2. Keep the scripted scene of him and some phantoms storming the Normandy to slow down Shep's progress in fighting the reapers so Cerberus remains a step ahead. Make him his own man again. Have him constantly harrass Shepard and kick the **** out of the squad by himself (and the gunship fire support) on Thessia. The same guy who made a habit out of gutting turians in Retribution with reaper upgrades should not be on par with Shepard. He should be like Bane (TDKR) in terms of unstoppableness. Have Aria storm Cronos with the Normandy and with her assistance should Kai Leng die a warrior's death. His fight with Thane should involve him moving inhumanly fast and blasting Shepard and co. when they try to interfere (think Wesker in RE5 when laying suppressing fire on Sheva aboard the bomber). Also give him a different voice actor like the guy who played Silver Lion in Man With The Iron Fists.
Wrex. Perfect in ME2. Stern, open-minded, ready. In ME3 there was waay to much jolly Wrex and smiling. It was off putting. Tone down jolly Wrex until after Tuchanka.
EDI. Ditch the body and the pinnochio story. Keep her as is in ME2, or don't sexualize her getting a body.
Legion, ditch the pinnochio story. Have the geth get subjugated by the reapers, not willingly submit. Legion rejects the reaper code but strives to push the geth to achieve such an upgrade on their own terms. Show other geth interacting with him to give insight.
Traynor. Tone down her role (give the option to recruit Kelly to the Alliance to keep her job as Yeoman on the Normandy). She should NOT be making the Shadow Broker look stupid and useless. Ditch the EDI obsession...