You expect a Regiment, without proper landing boats, much less amtracs, to make a successful combat landing on an Island with defenses that make Tarawa look like Disney World?
I'm not sure the Japanese could dig up enough extra rifles to equip all the assault waves they would need to expend to take the Island (actually the two islands, protected by a coral reef).
The initial IJN air attack didn't even scratch the defenses. The Yamato wasn't carrying bombardment rounds, neither were the fast BB escorting the Kido Butai. The expectation was that a short bombardment from a couple cruisers would do the job.
However, assuming the Japanese somehow make it work, after losing 5,000 or so troops in the process, Midway become the location where the IJN dies. Holding it would be a nightmare. U.S. subs could reach the area kill anything there (even with crappy torpedoes they would still get around 30% detonations) and be back to Pearl before the milk goes sour.