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See, I don't really watch anime for the filmmaking, I watch it for the storytelling.
In this I agree. There are some truly spectacularly animated things out there with lame writing to back them up. And like you, the appeal of PMK to me was the story, and also in a big way, the history. One thing I truly appreciated about PMK was its closeness to the historical subject at hand, whereas Kenshin barely pretended to be more than fiction in a period setting. Sort of like the difference between the darker, grittier Kenshin OVA and the lighter, fluffier Kenshin TV series/manga. It's true, PMK has its boy manga moments too, especially in the manga proper. If they left the Heisuke introduction, for example, exactly as it happened in the manga, then we'd have a lot of nonsense to watch. Funny nonsense, but nonsense still.
However, I think you might be a bit too harsh on the Kenshin series, in that while the early episodes were not as serious as say, the Kyoto Arc, it was good progression in its own way. I felt it was necessary to actually know the Kenshin gumi as we did through the first season, contrived histories or not, before we could truly enjoy the Kyoto Arc. PMK seems to be working on a different model, in that the main plot is the backbone from which all the character introductions and such spring, but PMK also must have a shorter, tighter (historical) timeframe to work with, being about the Shinsengumi. Kenshin had that small benefit of being in the Meiji, so everyone's dark past was related to the Tokugawa period. New conflicts had to be fantasized on the fly and strung together, which didn't always work to the series' benefit, and sometimes became utterly ridiculous (but somehow, always also at the points where the TV writers refused to follow the manga).
Back to my point, I think it's just the different story model at work rather than a difference in quality of storytelling/scripting/setup. I do agree though, PMK does, so far, look better organized plotwise, because it does appear to have a main plot as a backbone.
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My point is, physics-defying stunts don't either. Now, I'm well aware that 90% of the historical samurai shows ever made feature such stunts, but ya know - that doesn't mean they work.
Probably, again, the differences in personal taste quotient. With all due respect, as you've already said, 90% of historical samurai shows feature such stunts, and I guess it depends a lot on individual experiences with them. Stunts like that don't have to work, that is true, and when they fail, they fail hard. But the history of martial arts fiction is full of mad skillz, it's part of the entire appeal even, whether its in writing, animation or live-action shows. I think a large number of the enthusiasts expect their heroes to be larger than life, even if those figures are historical. And while realism is nice too, the point is, the superhuman-ness is a part of the experience and culture.
Which brings me to why I thought the magic use was the one that was out of place in a historical manga (stress on historical, since there are other period manga out there where the premise demands magic, like Inuyasha). Because like you, I did appreciate the realism inherrent in PMK. There is a vicious, cruel beauty behind the movements of the characters in battle, because of that extra human touch. Hitokiri behave like hitokiri, not heroes, and definitely not superheroes, and the actions define this brilliantly. And in spite of what I'm saying, I'm truly glad that this is the route the producers took too.
So that's why the necromancing bothered me. It's the wrong sort of anime, in my humble opinion, for it. Of course, this is still early in this particular storyline. They might actually make it rock, and I very likely will enjoy it anyway. Eh, but now I'm rambling into the unseen future. Hey, it's nice to hear a different view! Thanks for that.