This may be true - but I felt rather ripped off when I visited at the full price. I think I might have been happier if the exhibition at the Mori gallery had been more to my taste.

I think the models of various cities would be very interesting - This appears to be one of Mr. Mori's obsessions. Have you seen the website that his company created to compare the urban plans of the worlds great cities with Tokyo? I think this site was designed to support Mr. Mori's vision for Roppongi Hills and other developments. It's really fascinating:
http://www.mid-tokyo.com/

BTW - You can get a good panoramic "skyline" view of Tokyo for free at the Tokyo metropolitan government buildings in Shinjuku. Open seven days a week.

In the list of museums covered by Grutt, I would go for:
Edo-Tokyo Open Air Architectural Museum
Fukagawa Edo Museum
Tokyo Edo Museum (which you have already spotted)

As you can see, my choices are all on the same theme... and the idea of visiting all of those places in the space of one short trip... well I'd be happy but my wife would be furious if I dragged her along for that.

Actually, the biggest problem that I can see with the Grutt pass is that it may encourage you to spend your limited time in those museums which are included at the expense of several really wonderful places. For example, it misses out some of my favourite galleries such as the Ota Memorial Gallery (Near Harajuku - cute, small, Ukiyoe gallery which changes its display every month). And it doesn't include parks such as the Shinjuku Gyoen.