I was finally able to see this movie thanks to the Hong Kong blu-ray, and now I've watched it four times in the last few days.
It's definitely in my top ten Godzilla movies, and maybe top five. I've always had a particular interest in the movies that focus on the Godzilla vs mankind angle, and I've long wanted one that would consider the potential real world response in detail.
I can't believe this movie was possible on a budget that was 10% of Legendary's. Despite Toho's insistence that the puppet was never used, there are several shots of Godzilla's fourth form that are so convincing as a suit that I still can't believe they're CG. Also, the effects of the various tanks and artillery are practically flawless; only the helicopters look a bit off. The stand-out moment on the CG side has to be when Godzilla flings a bridge through the air; that just looks real. The miniature effects are also great, especially where we see roof tiles rattling (very reminiscent of the original Ghidorah movie) and interior rooms tipping over as buildings collapse. Higuchi may not have got to showboat on the creature effects, but you can see his hand in the quality of the miniature locations.
All the way through I had a nagging feeling that the plot of Shin Godzilla reminded me of something, and at last I realised what it was. The whole Goro Maki sub-plot is very similar to the first Patlabor movie. Both movies start with a scientist commiting suicide by drowning in Tokyo Bay. In both cases the scientists have set in motion a plan to destroy Tokyo after their deaths. So, in both, thwarting the scientist's plan means learning who he was, what he planned to do, and developing a way to counter it. Also, both had an element of turning nature against man (in Patlabor, a typhoon causes sounds that trigger robots to go berserk), and of unleashing giants on Tokyo (giant robots and Godzilla, respectively). Considering that the Patlabor series had a couple of stories that were direct homages to Godzilla, I'd say this is fair play.