You're better letting the council survive even as a renegade because it changes almost nothing. There's still 3 slightly different councillors next game and Udina is still in charge for the humans regardless.
Yes, but when you're roleplaying as a character instead of approaching things from an omniscient, meta perspective, it's fun to make decisions that are IC, even if the outcome is not optimal.
For instance, I prefer not to make peace between the geth and quarians. Adding more nuance to their conflict is fine, but ME3 went too far in the other direction by completely whitewashing the geth. You don't commit genocide by 'accident'. Besides, it makes Shepard a more grounded character if she's not magically able to resolve every ancient conflict by telling both parties to make up. Speaking of Udina, him suddenly turning into a traitor in 3 is silly. Him being the opportunistic contrarian who doesn't fawn over Shepard was more fun. Hell, have one of the Alliance officers who are always nice to you be the Cerberus patsy instead.
Honestly, I don't think Tali should've been a party member in 2. Her 'arc' feels like a regression. You meet her on Freedom's Progress, and she loses control over her team and needs you to fix things. You meet her on that other planet, and she's holed up somewhere and needs rescuing. Then she gets put on trial, and needs you to bail her out again. She's better in 3, but it makes her promotion to admiral really unearned after having been such a passive damsel in distress. Also makes the romance uncomfortable, honestly.
I'd have preferred her to cameo as a significant NPC and show she's making something out of herself among the quarians and trying to help you on that front (she'd have a lot more justification not to rejoin your crew than say Liara, who's not doing anything useful and trying too hard to be edgy). And have Daro'Xen be a party member in 2 (hell, have her be the one who was experimenting on geth instead of Tali's dad. She fits the geth expert role better. Tali's dad can simply be a hardarse admiral). Tali can then come back as a stronger party member in 3.
Shame the plot mandates you kill Tela Vasir. She would've been a neat party member/ally...if she'd kept her edge and not joined the 'cult of Shepard' (which, let's face it, most party members are card-carrying acolytes of). I could see Elpsis clicking with her.
As for Garrus, yes, he improved as a char and the romance is quite sweet. But...what is he doing on Omega? He knows the Reapers are coming and so he goes off to Space Tortuga to play Dirty Harry and kill some thugs. And just like in 1 he needs you to tell him whether to kill a criminal or not. I think they could've kept the Omega arc...but not have him throw the towel and go rogue because he was 'fed up'. He could've been there to investigate rumours of Collector activity, but when he sees all the injustice, he decides to 'expand his mandate'. His decision whether to kill Sidonis or not could be based on in which direction you steered him in 1 (I think if you don't import an ME1 save, the game just assumes you made a bunch of Renegade decisions, so default Garrus would be Renegade). And if you suddenly tell him to do something that's inconsistent, that affects what he thinks of you. Hell, maybe have him be involved in recovering Shepard's body.
Vega was just a stereotypical, disrespectful meathead. And while he's supposed to be the new guy and thus the audience surrogate for people who are new to the ME games...his ignorance is really over the top. Surely he'd know why krogans don't like turians. Being a grunt is not the same as being stupid. It's especially silly since his 'arc' involves being made an offer to join the Alliance's special forces programme...which would require brains as well as brawn.