Here are a couple of great concept designs from artist Danny Mora that feature Michelangelo and Leonardo brandishing more traditional ninja weapons and armor. We have yet to see what the Turtles will look like in Jonathan Liebesman's new Teenage Mutant Ninja Turtles movie. If they look like something along these lines, I will be very pleased.
I think armor and clothing would give some nice weight to the CG characters. I'd much rather see some progressively scuffed up clothing than pristine turtle skin the entire movie. Particularly in the Michelangelo design, you can also see that there's this romantic quality the flowing fabric adds to the piece -- much like Batman's cape in the comics and the Nolan films.