Should bioware do one final shepard game?

Yes.
First he betrays the Alliance by joining a terrorist organization. Then he betrays that terrorist organization.
And he acts completely self-righteous about it both times. At least Liam owns the fact he screwed up.

I don’t really have to deal with it. Jacob being the worst is confirmed by science. He even gets his own unique tier in any companion ranking, appropriately named “Jacob tier”. 

I think the writers of Mass Effect should really think about how they use certain terms in their story. Throughout all of the trilogy, the only time Cerberus could ever be seen as a proper extremist group is in ME3, but that doesn’t even count because they’re either indoctrinated by the reapers, or augmented thrall soldiers. Before that, we never really see anything that suggests that they engage in actual terrorist activity. They do a lot of goofy mad science projects that gets them in hot water, but most of that stuff is largely isolated that Shepard either deals with, or they nuke from orbit just to be sure. 

Actually the one situation where I would sort of be okay with Shepard returning is if it were a prequel. A Mass Effect Zero if you will.

It could create a ton of possible continuity issues though - plus the 'remake the trilogy' crowd would get uppity so I'm not sure if I would really want that.

You know what, you are right. I am converted. ME:A was the best ME game evarrr. Now, you and I must embark on a quest together, to convince everyone else that they're wrong. What do we do now?

Also three of them are imprisoned because of that. Joker only gets out because he was needed to work on the Normandy and was there when the Reapers attacked, and Daniels and Donnely are and stay there unless released by Shepard. 

That’s not really terrorism, regardless of the ethics, or lack thereof. 

The biggest problem is that the Council and Alliance do not have an appropriate response to Cerberus’ presence, and the plot makes everyone extraordinarily weak in order to justify forcing us to side with them. A ship emblazoned with the Cerberus logo should have been put on lockdown, and any operatives aboard arrested (and perhaps executed). But, we gotta hang with Cerberus because The Plot is our god. Even Shepard’s involvement should not have given an ounce of legitimacy to the group in the Council or the Alliance’s eyes, considering their involvement in numerous, forcibly-applied shifts in certain high profile figures.