I generally prefer the manga ( as it's normally the original form of the story anyway) and being a mangaka myself know that there is a stress about the issue over going to an anime format.
Biggest problem is that an anime following your series almost to the T will catch up with your current point FAST, so to buy time alot of studios add in alot of random scenes, and worse yet even entire seasons that are filler...not written by the real writer, not always approved by the writer, ( the bount arch, and several of the episodes over the last few months of bleach were fillers, and not considered cannon at all)
Now I get both manga, and anime straight from japan no subs, just as it is.. then see it later on " months or years later" in the West completely taken out of context and the language changed...
Now fair to say thats not always a bad thing, as some phrases, or context is something anyone in the west, even the most die hard otaku will have problems understanding, so they paraphrase it alot, though some series do this more than others.
when something goes anime it already faces a change while in studio...in the east, just like in the West...things aired on TV have to meet certain criteria, so to assure this the studio directors have to edit it down in content quite often.. then should it reach, lets say the states.. it has to usually be edited down further to be more people friendly by U.S standards.
Sometimes it's completely bastardized. Lets take Desert punk. In the manga it's a long on-going series that has a dark and very brutal overtone, it's quite violent, and forces one to really confront the darkest aspects of human nature...
however the anime version of it, though touching the main plot was converted to an over the top comedy rife with big boob jokes, and the " anime's" main character on an eternal quest to get layed, and get payed. then the anime abruptly ends after the first story arch, just as the serious nature starts to come into play. this was done to make it more " people friendly"
and lastly sometimes anime can just blow * even more when you have read a good series before it's made into a cartoon* is because often times the writer /creator of the manga series has not obtained the full rights to make the jump from one medium to another. that is to say a down and out studio has a intern obsessed with your manga...he shows the studio head, they decide " hey we can make this into a cartoon!" well guess what.. they can do so without ever going to you to get permission, and if they put out a half assed show of your popular title, your manga can suffer if its bad.. if it booms you don't see a dime, and it " ws" rare for court battles to go in favor of the manga creator. so for a time it was rare for a origional creator to have full rights over film, print, and marketing..one of the rare ones was Takahashi Romiko ( romiko takahashi) when she began work on Inuyasha she made sure to have her rights fully covered. Though there has been a move to change the japanese copyright system to match more of that of the U.S.
wow this is going on longer than I expected
but in closing I basically wanted to bring up SOME reasons an anime can be...less than great... when looking at it from a transition from paper to film.
and sometimes... a studio can produce crap, just like they can anywhere else in the world.
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