I've had only one map in mind that is predominantly based around water and where flag cannot be captured without going underwater, but only one. For the rest (in my opinion at least), it should play a rather minor role
you travel less due to the friction with it, so it's more of a liability (which it already kinda is, if you are against people who know how to act against ninjas)
woukd be funny if they could create when attacking at the end of their attack a wave that travels some distance and damages anything it hits with having half the damage with every continuous hit. just an idea.