I haven't read every post and I don't have a dog in the race, only logical non-emotional thinking, so maybe someone has pointed these points out already. Obviously, I'm not privy to closed door meetings, I just have public statements to go off of. After listening to the podcast, something really strikes me as odd that a lot of people seem to be missing.
1. Toho has the final say with who they want to do business. Not Spooky, not Stern. Simply being the highest bidder is not always the reason someone acquires a license. There are too many other factors at play especially when companies are presenting value propositions of why their company would be able to maximize a license. As much as Stern swooped in and grabbed the license, Toho decided not to do business with Spooky and chose Stern's offer instead.
2. Toho has indicated they want to expand globally. This directly contradicts what Spooky talked about in their podcast as they focused on the American market discussing how poorly Toho does in America. Spooky's podcast (around 7:30) indicated that the Godzilla theme does not match up with being a major title that will sell thousands of games in their view. Spooky gave no indication that they would move to mass produce games on a global scale for this license and push into foreign territories as around 15:15 they mention there's a non-existent pinball market in Japan and that the game will be aimed at American audiences. Again, this directly contradicts what Toho has stated publicly their intentions are with this license on various products and expanding to other marketplaces. Basically Stern is going to enter an arena that's completely untapped.
Toho's goal isn't to provide their license to a business that really wants it. Toho's stated goal is to focus marketing activities towards the Tokyo Olympic Games in 2020, expand into China, and expand into a global market. This includes using new avenues to allow Godzilla to reach new demographics, they've said this repeatedly in interviews. Again, which company is in a better position to begin further expansion into the Japanese and Chinese demographics with a top tier license for that area? If you're Toho and looking at the portfolios of both companies, who do you have the most confidence in moving forward? If you're Stern, what better theme is there to introduce into these markets?