I think they pretty much had to leave Scott in a bad place in this series so that there'd be a reason why Wolverine is leading the team instead of him. Although really, if Scott were too screwed up to lead, then Storm should be leading. But when Charles put Logan in charge, Storm was gone. I guess.
I find the level of property damage inflicted in this episode to be implausible. The repair costs would've run into seven or eight figures, there were probably numerous injuries, and Scott could've easily killed people by blasting through the pavement from below without having any idea who was up there. By all rights, the MRD, the National Guard, maybe the Army would've been called in as a response to these events. This is a major disaster caused by one man, and it shouldn't be just forgotten about. Certainly not by the X-Men themselves. Scott's negligence and destructiveness here were criminal, and he should be held accountable for it.
And why is Jamie Madrox one of the bad guys? I guess because he was a bad guy in the third movie -- but I don't get why he was a bad guy there. Did he go through a bad-guy phase in the comics? Although in both cases, maybe it's just because his power makes him a useful adversary for the heroes.