well, if you're looking for a constructive point of view, here goes.
personally, i love the comic format. you can really drive home the feeling of intense action packed events, and you put in alot of details that normally wouldnt be feasible in a OC flash duel (considering the deadline and everything)
however, there seems to be a pattern springing up, with judges voting against you for the entry being too busy, somewhat cluttered, and difficult to read (personally i had no problem reading it, but thats just what i hear). your flash entries really have none of those difficulties, so it may be a smart idea to take up flash in your entries again for the next tourney you participate in... (maybe im assuming too much, now that i think about it, i dont actually know if you joined a new one)
Hard choice, both mediums give different results when looking at content and such. For an actual story though, I guess comics would be better, flash can sometimes get a bit gimmicky but comics can be more detailed and creative. I'd guess that either medium would be batshit-crazy and fun, but I'd have to side with comics.
Although I voted for flash you should defenatly keep working on your comics aswell because they're of a superb quality and by that I don't just mean the artwork (christ I sounded like a posh toff then -_-; ).
If you don't mind I have a suggestion for yourself please tell me what you think-
One way that I think that you could go about it is - well for the (how can I put it) 'main body' of the story you could do it in comic format as it'll be no dout easier on yourself and your 'work load' but for main battles, duels,epic fights etc. like erm... I dunno... Spoiler vs Black Ace (I'd bloody pay money to see that scrap!) could be done in flash as you'd no dout be able to fit a lot of action into them.
Take note or just ignore me your choice (don't intend to sound mean then) but then again like I said it's just a suggestion and like *spookydoom said "Whichever's easiest on ya' dude."
All I can really say is keep on animating 'n' keep on doodle'n as long as you see fit Zeurel.