If you look at the huge franchises from 15-20 years ago, the ones that are still strong today, they're all Japanese franchises, and only the ones that become too westernised or too big-budget end up weakening. Final Fantasy peaked somewhere between 7 and 10 (opinions vary on this), as the budget for the games continued to grow. Resident Evil seems to have peaked at RE4... RE5 and RE6 both look like they'll perform more weakly, due to increased budget.
While it's true that the tendency to work with anime-type IP is harming their popularity outside of Japan, the essential Japanese-ness of their big games is one of the big draw points, that set them apart from Western developers.
Here's something to consider - one of the bigger recent franchises is a split-off from Rayman. The Rabbids franchise is exactly the sort of thing that should be coming from Japan - it's just so zany, unrealistic, and focused on fun. But imagine what, for instance, Square Enix would have done with the idea - the Rabbids would have looked very "realistic" with ear physics and fur simulation, there would have been heaps of dialogue, and the gameplay would have ended up being very bland and formulaic.
Another example of what SHOULD be coming out of Japan is games like Red Steel - games that try to put a distinct Japanese spin on classic western genres. Again, though, imagine what current Japanese devs would have done, and you'll see the problem.
There are certain genres that the Japanese developers stick closely to - the RPG is the biggest of these. And that's part of the problem - when you have an entire nation of game developers making pretty much just one genre, there's going to be massive competition, and sales will be weak for all of them. And then only half of them make it out of Japan, with relatively little fanfare.
The talk about Japan following the "hollywood movie model" scares me - hollywood is formulaic, has oversized budgets, rejects innovation in favour of what has always worked, and prefers gimmicks over substantive changes. And I think we all know which publisher fits that description. What Japan needs to do is follow the Japanese tech industry, known throughout the world.