Having no really fast startup aerial to break combos really hurts vs ness. At something like battlefield, his killing consistency is painful. That said, mobility is so key that I do think ninja wins. Its close though. Your dashgrab basically can't be reacted to, so getting grab conversions is key. However, he does have an amazing airdodge and aerials to break out, a well timed AD-> nair will break your usmash. Of course, it can also beat the fsmash trap with good timing and spacing, which is frustrating. You won't see too many really skilled Ness, but when you do it can be disheartening. Not having a hitbox on our recovery is annoying vs Pk thunder, but he has to be careful of SSBackstab, Counters, and rising fair. On the other hand, we destroy his recovery with relative ease.
With his good airdodge and accel/deccel/aerials, I prefer to play a horizontal game. as someone said, fair is really really hard for him to do much about. A mild read to hit him out of his double jump can often mean death pretty easily, fair and bair together are great at that.
When he is FH in neutral, or if you have high rage and he SH even, a well aimed hydro pump spurt can suddenly put him in a landing situation ala fludd. This is powerful vs most characters, ness is no exception.