Uhm, I've heard of one show, Zipang, that's supposed to be a time travel alternate history study of WWII Japan, but I dunno much about it.
I've seen it. Last time I checked there was only one season available, which left the story in a pretty much unresolved state, with no second season in sight.
Anyway, do you know that cheesy american movie from the 80s - "The final countdown"? In which, an American then-modern carrier goes back in time to just before Pearl Harbor and plans to show them the American way and divine justice with all that superior technology*?
Well, this is exactly the same story, only made with the Japanese audience in mind. Which means that we get a JSDF AEGIS-class cruiser going back in time, and kicking the yankee butts, only with more "what's the right thing to do" pondering, which is a welcome change from the previously mentioned film's attitude of "hell yeah, let's do it!".
Ironically, the ship is built with probably +90% made in USA technology, when you think about it.
And without spoiling much, I can say that it doesn't go back.
There isn't that much of an alternate history here, in the end. The most promising arc in this respect is only signalled at the very end of the show, and left to develop in the, as of yet nonexistent, sequel.
The best parts, apart from showing off the capabilities of moder technology, are probably when the imperialistic mentality of the characters native to the timeline clashes with the mentality of JSDF servicemen.
There are some cliche things too. Most notably, Yamamoto is completely dehumanized, and presented as an almost saint-like figure, which appears to be notorious treatment for notable people from Japanese history in this medium. Also, the Americans are so stereotyped that it's almost comedic.
It's a good watch, all in all. Gives some food for thought, but not as much as it potentially could. And, you're bound to be left with a cliffhanger of sorts, by the end.
http://www.animenewsnetwork.com/encyclopedia/anime.php?id=4649*I don't think I'm going to be generalising too much by saying that every boy dreamt of something similar, taking modern weapons to the past and kicking arse. I remember that I wanted to have a machinegun at the Battle of Grunwald(aka Tannenberg).
Re: Jin-Roh - it's a really great film, I highly recommend it, even though it's not really military-themed. More like military police-themed. The plot is concerned with fighting dissidents, and internal struggles within the secret service ranks. The fact that some of the operatives use heavy combat equipment is just an artistic touch(or more like Oshii's pet peeve, I suppose).
High production values, hyper-realistic art designs, haunting music score, and a challenge for your brain cells. Worth watching whether you are an anime fan or not.
One other military-styled show that I can think of: Area 88 - an oldie(oh, the hair!), about mercenary jet-fighter pilots.