Tokyo SOS has the best special effects of the Millennium films, so it has that going for it.
I also kind of liked how they tied things to the original Mothra film, including bringing Chujo back. That was a nice touch.
It was also kind of neat that basically the whole back half of the film was one long monster parade. It wasn't a handful of battles in different locations, but rather one really long and changing battle in one location, which was actually kind of neat.
Being honest, Against Mechagodzilla isn't one of my favorites, mainly because the movie didn't payoff most of what it had set up and barely stands on its own. This film, at least, tries to follow up on the Kiryu is alive idea and provide some closure to that. And at least the debate of whether or not it is even ethical to have this thing is handled a little better, as opposed to the last film where the only person arguing not to use Kiryu was a little girl who thought her dead mom was a plant. (Yeah I'm mean, sue me).
I guess if there is anything wrong with Tokyo SOS, it is that Mothra's inclusion in this film feels like a greatest hits album of her previous work. Basically almost everything she does in Mothra 61 and Mothra Vs. Godzilla 64 is repeated here in some way shape or form. I actually would have liked for there to be more of a payoff to Mothra's opposition to using undead Godzilla as a weapon by having her and Mechagodzilla actually fight at one point. That's never happened on screen and it would have been neat, and it would have given us a three way monster battle, as opposed to Godzilla Vs. Everybody, which we already saw in GMK.