Biggest difference to me is that Bionicle's aesthetic, while not always in line with 2001, had certain themes that were definitely there consistently. I think LegoDavid summed up the Ninjago issue perfectly just above:
It's not that the "Ninjago style" turned out to be different from what people were expecting - I'm all for sci-fi ninja if done right, sounds epic - but there is no Ninjago aesthetic. Sometimes it's modern, sometimes it's oriental, sometimes it's magic, sometimes it's futuristic, sometimes it's literally video games. About the only thing in Ninjago that you could say is there every year is... well.. ninja, and even then in some years (coughRebootedcough) they haven't even looked all that much like ninja (although I'm aware actual Ninja didn't really look like that, but still).
The only thing I really enjoy about Ninjago still is that they're doing really well is detailed part design, especially when it comes to minifigure prints. Some of them lately have looked totally awesome.
I wasn't actually around for Ninja 1998, but a quick google suggests it's probably more up my ally (if a bit dated). Probably my "dream ninja theme" sits somewhere between the two, but it's definitely more Ninja than Ninjago, personally.
tl;dr: Exo-Force beats both and is Lego's best oriental theme.