What do you want?

This is just me, ME1 and ME2 version Of Cerberus is what I truly prefer and a much smaller organization than what we gotten with ME3 version of Cerberus due to the stupid big it has gotten within ME3 at an unreasonable size unreasonably quickly. Also My ideas with Cerberus would be less of Incomptence Inc. and more effective organization(less of them fucking up and them making effective science projects of all stripes). 

With my idea of ME3, Harbringer thru various means Reduce Cerberus to 1 to 2 Cells. Also I would have Harbringer have a much bigger role and having several plots in motion that causes massive damage to all canon factions thru Reaper Sleeper Agents, Classical Reaper Husks and Collectors.

Also If there are going to be more humanoid factions to shoot up outside of Reaper(both Classical Reaper Husks and Collectors) and Geth, I would love to see someone add new Factions or develop under used factions.

For example, Reaper Sleeper Agents can be made up with Several Known factions(alliance, citadel and other canon factions). Imagining fighting against Indoctrinated Justicars or Quarians or Alliance Marines for various quests. Or forced to Fight both Krogan and Turian Reaper Sleeper Agents On Tuchanka Arch.  or get into a crossfire between Geth and Quarians and both of them actively shoot at you.

Sorry, just addressing this part. I think Cerberus was still too big in ME2. They had the money to spend billions of credits to resurrect Shepard and restore him to prime condition. That money couldn't be easy to come by, at least not without basically shutting down every other cell to make it happen.

They were unreasonably large even in ME2

Mass Effect: epilogue

Entire game made to deal with ME3 aftermath 

You can have Liara and for science you can have your way with her

I went with MEA2 with new protag simply because I am dying to see Andromeda/Helius 100-200 years later, getting to see the fruits of Ryder and Co.'s labor.

I think a ME3 with one or two more years of development and less reliance on sets of MP faction units for combat enemies, could have at least been a lot closer to this concept that I agree with you on

I wanted way more Indoctrinated, by the Reapers directly. Not because I'm totally in love with this idea, but because its what the previous games seemed to be setting up anyway. I feel they rolled up too much into a Cerberus faction, and maybe it could have been done better and more enjoyable, but it wasn't so bleh.

It was not a complete failure.  You are welcome to not like it, but if it was a complete failure nobody would like the game and the way people talk around here is enough proof that isn't true.

I'd rather a sidequel set in the Shepard era set on Illium, Omega, the Citadel, or Palaven. Something other than a party based RPG (please don't jump on my back, I ALSO want a proper Masse Effect game too). Maybe a stealth based espionage thriller about an operative for the Council on a mission that will earn them spectre status? Something set between two of the original three Mass Effect games?

The problem I with any game that will take place before the end of Mass Effect 3 there really isn't that much to tell, its not like something like Star Wars where you can set something about the Force 10,000 years before the movies so anything you do doesn't have to match up perfectly with that information.  The other problem is BioWare doesn't have the skills for those types of games and the more people complain about Anthem the less hope I have for them to even try to incorporate those ideas into existing franchises "because it isn't BioWare".

Again that is personal opinions then, for people have been ranking the game differently from its launch for not everyone feels the same as you.

I thinks there's plenty to tell. The primary reason Mass Effect is such a great series is that as important as Shepherds story is, it doesn't happen in a narrative vacuum. There are all these different governments, and corporations, and organizations, and characters, all vying for resources or influence or agendas with nothing at all to do with the Reapers or Cerberus.