Junpei still "speaks" broken English even when he's speaking Japanese.
Did it ever occur to you people that speaking kung-fu/ninja/old samurai movie/monster movie english was not just bad dub work but that was really quite accurate? Maybe that how talk in native language too? Its a JOKE people. Its a deep joke about stereotypes and slang and accents and how people sound.
People from tokyo consider a Osaka accent to be heavy, much the same way a midwsterner would look at a western accent or new york accent. When dubbing Japanese shows into english, It makes me cringe when they use a texas accent or a new york accent to translate osaka-ben. Having a character speak with a southern or a new york accent does not simply say 'this character has a different accent' - it carries with it all the connotations of that accent we are familiar with.
Junpei speaks in bad movie english in english and japanese because its works with part of the whole 'ninja' thing in megatokyo. I'm making fun of it, to a point - making fun of the ninja stereotype (since when would a real ninja EVER wear a shirt that says 'i am a ninja???') Remember those Lipton Brisk Tea commercials? "Editing mistake in my favor!". Ya, funny stuff. you make fun of it because it is so fsking cool :)
People who get all worked up over the mechanics of the brackets and translation system in Megatokyo are doing just that - getting worked up over mechanics, and need to lighten up and go with the flow. It's a lot like the "OMG, how can you put 'genki' within the brakets! its japanese! you need to break up the brackets..." <--- I have resisted urge to smack people who get on my case like this.
Junpei is not like L33t Dude, where the contrast between what he says and leet and the prim and elegant subtitles are all part of the humor - a huge shift in how junpei talks would be jarring, never mind the fact that i am doing it for commedic effect and as commentary on the inherent problems with any sort of translation. I think people can deal with the mecahnical paradox if it helps me keep Junpei who junpei is.