"Kiss your plot goodbye. Here's loyalty quests and non-important companions!" paraphrased: Mike Gamb

Can't really fault him specifically for loyalty survival. Most of them have this problem. One of the worst is Zaeed, albeit something that happens in ME3.

Except the Council's "official investigation" was clearly a farce to save face and appease the humans demanding something be done, especially given that C-Sec were actively stonewalling Garrus so he couldn't find any evidence, even if it did exist.

He was supposed to conduct an investigation into charges of Saren's corruption or involvement in the attack on Eden Prime. With all of Saren's work being locked up tighter than a Nun's chastity belt in a brothel,  how did the Council expect him to find anything when Garrus wasn't given the necessary clearance needed to look into those files?

The obvious conclusion is that the Council never intended to do anything about Saren and were trying to sweep the entire matter under the rug.
With Shepard's death and the Council whitewashing events (again) so that Shepard was delusional and Sovereign was a "Geth" ship, it's not hard to imagine that Garrus might have been blacklisted by the Council and C-Sec.

Without proof or political clout, there was nothing Garrus could do by that point... at least, not unless he set up a soapbox next to the Batarian Preacher and began ranting about Armageddon? In that circumstance, I'd see shooting criminals on Omega as way more productive. People might be doomed, but he could ensure they wouldn't be mugged.

Following ME2, it took Garrus' father calling in some favours before he was able to get a token task force assigned to him. Even that only was achieved because Garrus had amassed enough evidence by that point convince his father that there was some validity in his claims.

I think you're overreacting.  The key word in the segment that you emphasized in bold, is "entirely."  Moments like those on Virmire were not character-centric, not in my opinion.  Wrex's confrontation only really showed you how far he was willing to go for his people, which lacks a lot of gravitas if you never talk to him on the ship.  Also, choosing the Virmire survivor had nothing to do with Kaiden or Ashley's history as characters.

I think what Mac Walters is saying, and what you're subsequently overreacting to, is that loyalty mission put their respective character at the forefront of that mission's narrative.  It doesn't mean that they won't get focus outside of these missions.  It only means that they'll be sharing the spotlight with the rest of the cast during the main plot.  I mean, this is what mostly happened in Mass Effect 2.  Garrus had brief moments to himself in the game, but he was at the sole focus of his loyalty missions.