The IJN (while formidable) is on the wrong side of the planet.
And even more to the point, not as good as they thought it was [1].
However, one of the more damaging characteristics [2] of the Nazi government (and to a slightly lesser extent the Italian fascist and Japanese governments) was obsession with competition for its own sake, favouritism and rating political acceptability and loyalty above competency. Collaboration, trust and sharing will not thrive in such an environment and are likely to be viewed as signs of weakness.
Add to that that if the IJA and IJN struggle to cooperate, if the Luftwaffe, SS and army all have their own command structures, and if the nazis hate and despise even their own European allies, then what chance could they have of strategic cooperation going beyond a few insincere words at state visits?
[1] Perhaps it was, for a time, extremely good, but had insufficient depth and resources to stay good.
[2] I suspect that viewing (some of) your countrymen as a superior race to everyone else would also create a barrier to collaboration with people who - under this distorted world view - must, by definition, be inferior in some way.