I have no preference either way, personally. I understand what each take represents (all-red is their "clan color" while the multi-color ones are so kids can tell them apart) but I'm pretty easygoing about it and don't mind whichever. The Mirage comics where black and white, anyway, so it's not like their having red bandanas in that title mattered. Even if they'd had multi-colored bandanas, you still wouldn't be able to tell them apart unless their weapons were showing.
I'm sure more than a few adults back in the day were appreciative for any cue they could get to figure out who was who...
I prefer the individual colors, though. Besides reflecting their personalities, in a way, it really is their most defining feature.
Actually, I rather enjoyed that the Archie comic had it where they did all wear red initially, and Splinter couldn't tell them apart... and, if memory serves, they used
that to their advantage... against their enemies and Splinter!
But even so, they eventually got to their trademark colors.