Now that you mention it, I think it would've been much better to have Akise as the main character. Think about it, a show centered around a detective trying to find out the mystery behind a manhunt between a diverse cast of crazies and ordinary people prepetuated by an unknown entity. That sounds much more awesome than watching Yukki huddle in a corner and cry as he has Yuno be his pet dog (seriously, she only loves her master, she will snarl and attack anyone that gets near her master, and her basic vocabulary consists of the word "Yukki". She is seriously his pet dog) do all of his work for him while she continues to slowly ruin his life and friendships, not to mention she kept him in captivity in an abandoned building. Hell, at this moment, I would have much rather had the "Lovey Dovey Couple" just murder both Yuno and Yukki than give them a chance to recover after Yukki sniveled and cried about how pathetic he is after not protecting Yuno from the fire.
As for Shu, none of the GC characters are written well, but that's the reason why Shu is somewhat more bearable, because the writers never fully understood whether they wanted him to be courageous and strong or weak and beta, so it pretty much wavers back and forth and switches from Lelouch to Simon to Shinji depending on how the writers think he's feeling at the time, while Yukki slowly gets more and more pathetic by the minute. There are just less times when the writer feels generous enough for Yukki, hence why the only time Yukki was actually awesome was when he told Yuno to go to Hell, but they screwed up real good by just having to keep Yuno by Yukki's side regardless of whether it was actually a smart decision or not.
When it comes to Durarara, I know you hate this argument alot for why I didn't like the 2nd half, but when it comes down to brass tacks, the Yellow Scarves story was all about Kida, and as such in the anime adaptation should have been about how Kida was handling not being able to control the gang he started. Instead they try to add all this bullcrap about Mikado wanting to take down the Dollars, even after they all banded together to save Anri from getting in Horada's hands. I would say that Kida running away from his responsibilities was also very lame (especially how he felt about Anri'), but he redeemed himself somewhat when he barged into the Yellow Scarves compound right when Horada ordered his execution to kick the **noel** out of his own gang and returning to Saki. With Mikado though, he just let the Dollars get their **noel** handed to him, and when he had the cards to keep them protected, he kept going back to bawing about how he wants to disband.