I personally do find the Ninja abilities overrated.
Stealth Jump could potentially allow you to jump more often. However, if it is safe to jump anyway, then the jump delay added by the ability is a penalty with little benefit.
Ninja Squid is simply a virtual speed limit on your swimming. You can accomplish the same effect by just not swimming at top speed. If it made you stealthy on walls (which it doesn't), that would be a different story.
All this said, most of the abilities have minor effects as well. I am constantly trying new combinations and always seem to find something fun. For example, special duration up has surprised quite a few opponents as they try to outwait my bubble.