I think the whole idea of crossovers is to put together characters from two completely different worlds into one game. I dont think they're supposed to be from similar worlds. The fact that Lars isn't really a ninja and comes from a completely different type of world makes it more interesting.
I don't know, I myself prefer crossovers where at least the two (or more) things crossing over at least have something in common to bind them.
For example, the Star wars characters in Soul Calibur 4 are really really out of place for the setting hence it's a bad crossover where as having the guy from Assasins creed makes more sense because he's from the same relative time period.
As you said Lars isn't a ninja and he has nothing in common with Naruto's world and so feels really really out of place.
The absolute best ones are stuff where things go together really well like Avengers/Jla or Batman/Spider-man