Some of this isn't SOA's fault though? From what I understand, the deal with Colonial Marines was more that Gearbox were dicking around and using money Sega gave them on Borderlands, then outsourcing it, then producing a trailer of lies, and finally Gearbox had to get a game out the door. That last stretch was mostly SOA demanding a release since they likely had contracts to fill and just wanted the game out already, but I think it had more to do with Gearbox just being distrustworthy and lying.
Toejam and Earl got mentioned somewhere in here, like how a DS game was proposed but rejected. From what I understand, Toejam and Earl 3 sold horribly, and they were pretty much a dated concept to begin with, so their rejection of it I can understand. This was during a time when Sega as a whole was still trying to recover from the fall of the Dreamcast and near-bankruptcy, so a game that sounded like it might be a failure would be something they don't want to put too much money into. Same reason they produced decided to forgo a new Jet Set Radio and instead make a new House of the Dead, it was simply a better business decision at the time. Also, they DID manage to get Toejam and Earl for All-Stars Racing, but by the time rights got secured, it was too far in development to add them. I assume the same deal went down for Transformed.
Beast Riders was a shitty game, there's no dancing around that. But Beast Riders was six years ago. More intricate fuck-ups have been made since a bad reboot. SoA's fault? Probably, but they've made worse decisions since and I dunno why you're still hung up on it.
Vector Man 3 was, again, likely going to fail (aren't the original Genesis games somewhat obscure now?) so they never went after it.
Mis-marketing of games has been a huge problem for SoA of late, I won't deny. I think they would be much better off marketing the relatively cheap to make HD re-releases of games more, and starting to branch out into letting other games breathe. A good marketing campaign can make or break a game, though they seem to be doing well enough not marketing them (The Typing of the Dead Overkill and Valkryia Chronicles PC have apparently sold very well despite really any marketing whatsoever), so I could be wrong.
As for Yakuza, well I can only assume its lack of appearance in the west is due to some sort of xenophobia and trepidation around very Japanese-centered games, as in games taking place in Japan. You'll recall quite a few games from the 90's up to the aughts getting a treatment to hide the fact they're in Japan, and this trend has only really started to lose itself recently, since I would say 2007 or 2008-ish. Which just leaves the xenophobia.
Bringing unproven Japanese games to the west is always a gamble for any company, for a number of reasons, and that's all I got to say on that.
Some of it does put the blame entirely at SoA's feet, but SoA is also a business, and a business arm of a company that's struggled since the mid-90's and has only recently come out of a slump. Sometimes fan demand can't be met because you need to pay bills, no matter how much you want to make that game.