The funny thing is, I remember this one pretty fondly. It was the last Heisei I managed to get ahold of, and I generally enjoyed it. But on this most recent rewatch, it just... didn't have that much there.
On the plus side, the human story- while still a bit broadly-sketched- is one of the more likably engaging human plots. The characters are still a bit broader than GvB and GvKG, but their relationship is also more enjoyable than the angst of vB, the shenanigans of vKG, and the cartoonish bickering of vM, at least to my mind.
And, heck, I like baby, and that plotline... Godzilla gets good action throughout, including a surprisingly-brutal fight with Rodan right near the start... this one ought to be a winner. But it came across as... just okay.
Part of it is, with the introduction of Baby, Godzilla becomes the sympathetic character; I'm not really rooting for Mechagodzilla. Also, the second-brain bit arguably (one could argue it started with ANEB, or even way back with the Oxygen Destroyer) introduces the trend I detest of 'We have this surefire Godzilla-killer (zapping the secondary brain, blood coagulant bullet, Dimension Tide, Absolute Zero Cannon, etc.), and we spend literally the entire movie just trying to successfully aim it at this slow-moving, skyscraper-sized target, or we use it but a Deus-Ex-Machina undoes the effects.' It makes Godzilla feel oddly vulnerable and weak- you're almost afraid for him, at the hands of humans, and that's not the right tone for a G-film- and it makes the humans seem incompetent, that they have a kaiju-killer but have to struggle through so many shenanigans and delays just to deploy it. As a plot device, it just doesn't work for me; and here, when it seems like they're practically torturing him (to try and finish him off), and essentially keeping him from his child (even though he doesn't actually decide to adopt until the end, with a little nudge from Miki)... well, I'm actively rooting for Godzilla to smash his doppelganger into scrap, and I don't think that's the way it should work.
It's fun to see Rodan here, and I'm of two minds about his use. Obviously, the Heisei suits don't permit the same running, kicking, and punching that the Showa era did- thus it's mostly full-body grapples and awkward tackles (perhaps this is why Shin Godzilla is downplaying his arms; he can't do much with them!)- and in that context, it's surprising how vicious and effective they manage to make the fight with Rodan. At the same time, they do feel the need to give him a beam-powerup, just like Mothra... and I think it goes to show how the old physical fighters of the Showa era just don't fit as well in this energy-heavy, ray-dominated era. They were infantry- but Heisei Godzilla and most of his new opponents are tanks. Well-armored behemoths shooting heavy weaponry at each-other. Scrappers need not apply.
Sadly, I think this is the weakest of the Mechagodzilla iterations, because the through-line of the plot just doesn't engage us. MechaGodzilla's not the unquestioned villain to be defeated; he's not involved in an interesting ethical dilemma... here, MechaG comes off as just kind of a jerk, yet ostensibly piloted by our 'heroes.' Godzilla is stuck straddling the line between evil-menace-to-be-stopped in the previous films, and sympathetic-parent/defender, as in the next one (or Showa series), and the off-balance emotional cadence of having trouble knowing who to root for really makes this one harder to enjoy than most, despite all the things it does well.
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