The tri-cools aren't bad on medium on noise or performance in mine, I still use 5 of em, up to you I guess.
The big boy on top and the ones in the rear are kinda hardwired into the case, but if your into modding in the first place probably not that big a deal. The ones on the drive bay cages have controllers in the front for them, also wired to the fans I believe. I'd never tried to remove them, so not sure if there is a plug or hardwired in.
I've seen a lot of them that have been modded I guess, but I still use the stock ones.
Pretty much I'd say unless your very picky about your fan volume there isn't too big a reason to go bananas with the stock 1200 fans, less ya like rewiring the whole case but for a new build to each his own I suppose
I'd try the 1200 fans out first myself if I where you before you went too nuts, as it has manual speed control on all the external one's to begin with, one of the reasons I tried the case out to begin with.
Plus they are non-clear and LED (the LED thing really wasnt an issue for me to begin with, but its worked pretty well with my overall color scheme I guess
)
The ones that come with the case aren't really your typical tri-cools, I have a few clear tri-colored ones myself in a drawer over here. I imagine the guts are similar, but still I'd give em a shot before you go too crazy replacing and rewiring at least 5 fans.