The Ronin storyline exemplifies, for me, the central flaw in Saints Row 2's storytelling. It has a lot of promise and the voice acting and presentation are impeccable, but it is so thoroughly steeped in the game's contradictions that it winds up falling flat.
Let me start with the good. The Ronin storyline has my favorite moment in the series (and possibly in all of gaming). Your lieutenant, Pierce, is explaining his elaborate, Ocean's Eleven-style plan to rob a casino, complete with a scale-model and split-second timing, and then Johnny Gat saunters over and proposes an alternate plan - rolling up to the front door and killing everyone between the Saints and the money. At that point, I wanted to high-five the television. It just perfectly encapsulated my feelings. Your characters are impossibly bullet-resistant and immune to legal consequences, so why shouldn't they act like it? It really was magical.
I also really liked the complex three-way relationship between the Ronin's leaders. You have Kazuo Akuji as a stern, unpleasable father and his son, Shogo, is this gross, irresponsible playboy (but when you see the two together, you can definitely see how he got that way) and then added to the mix is Jyunichi, who is stoically loyal, even to the unworthy Shogo and who Kazuo treats like a second son. I would definitely play a whole game centered around these characters. The scene where Kazuo is mourning Jyuinichi's death and spurning Shogo's attempts to emotionally connect with him is just great. The script, the animation, and the voice acting do a great job of conveying, in just a few minutes, who these people are and what they mean to one another.
However, this touches on the main problem. As good a story as it is, it doesn't really belong in the Saints Row universe. And to see why that is, we have to look at the central event that drives so much of the Ronin's story - the death of Aisha, Johnny Gat's girlfriend.
It's a moment the series tries to wring a lot of pathos out of, not just in this game, but in both of the sequels and the standalone expansion to SR4. And it's not difficult to understand why. The Saints Row series is nominally a crime drama and "male protagonist is motivated by the tragic death of a disposable female character" is hard-coded into the genre's DNA. However, I feel like Saints Row never really earns that pathos.
When we first see Johnny Gat in SR2, he is being sentenced to death for 300 counts of first-degree murder. Now, sure, a lot of those were gangsters, but a significant number were police officers (and that total was immediately increased in the course of escaping the courthouse), and considering the way the Saints fight, there were probably also a few bystanders as well (we might also count pedestrians among the total, but I'm not sure whether the Boss's driving is established as canonical before SR4, and it may be that only they are so bad at it that the Hague had to set up a traffic enforcement division). Many of the people Johnny killed were someone else's Aisha.
And while you could definitely make a compelling human drama out of the sort of hypocritical blindness that sees strangers as totally expendable, but the loss of a friend as an unforgivable tragedy, I don't think Saints Row 2 is up to the task (and, indeed, is at its best when it manifestly isn't).
Take the character of Aisha. If you read her in a straightforward, literal way, she is a monster. She loves Johnny Gat, and is under no illusions about who he is or what he does. He kills a captured Ronin in cold blood, right in front of her and she hands him a mop. She isn't even nonplussed. The only thing that alarms her is the fate of her floors. And when you consider that she allows the Saints to (admittedly temporarily) use her house as a waypoint to launder money stolen from the Ronin, she looks less like an innocent victim, tragically caught in the crossfire and more like a legitimate target who just so happens to be important to the Saints' second-in-command.
What we have here is a situation where it's reasonable and logical for Johnny Gat to react to her death with anger, but absurd for the viewer to take the protagonist lens at face value. Saints Row 2 isn't deft enough to pull off that sort of nuance, though, and I'm pretty sure it's not actually trying to. Everything about how the events are framed establish this as a run-of-the-mill "badass's girlfriend gets fridged" moment.
By the same token, evidence suggests that Aisha's inhuman callousness isn't really meant to be taken seriously. Before her death, Aisha is aggressively normal. Everything about her, from her conservative style to her posture to her house in the suburbs, projects an image of middle-class stability. Taken in the light of her backstory as a successful pop singer who faked her death to get out of a contract with a corrupt record company, and it's clear that she really is meant to be a "regular" person and it's just the Saints Row universe that is morally absurd. Aisha can be an innocent victim because she lives in a world where costume shops advertise on the radio by bragging about how useful their masks are for robbing banks. Indeed, it's revealed in Gat Out of Hell that she makes it into heaven. Let that sink in. The God of the Saints Row universe is totally gangster.
Which is, you know, funny. Aisha is a funny character. Just like the fictional show "Fuzz" is funny. Or the way that the cops want the Boss to autograph their gun before surrendering is funny. Yet her death is not funny. And it's never treated as funny, even as the sequels become much sillier and morally nihilist. This event is like a scar running through the series, part of the growing pains as Saints Row transformed itself from "slightly goofy GTA clone" to "all out bonkers genre pastiche."
The internal tension of that identity crisis is what defines Saints Row 2 for me. It's a fascinating game, but it never quite finds itself. That's why I think it needs Saints Row: the Third as a companion piece. Otherwise it's a setup without a punchline.