Because It was baaaaaaaad
As far as "Less effort" being put into Ninjago, its really not hard to see why. Batman and the overall LEGO brand are both massive cultural juggernauts. Ninjago, despite all of its success, is only one part of the massive LEGO library.
As such. You can't blame Warner Bros. For not wanting to pour all of their time, money and talent into something that wasn't guaranteed to be a hit.
Plus, with both TLM and TLBM, the cast and crew were approaching the projects with a lot of passion and history with Batman and LEGO. However with Ninjago, it was more of a "Oh yeah my kid loves Ninja-gos" Situation. They didn't understand how to handle the property because they didn't understand what makes it special and what makes it tick. After all, they didn't grow up with Ninjago, and most of them didn't have a part to play in making the original show.
It would be kinda like if I had you make a He-man or G.I Joe flick. You've probably heard about those franchises in passing, but you and most of your hypothetical crew would probably be pretty ignorant when handling a property that you don't have that investment or attachment for.
As far as a second LEGO Batman movie is concerned, it gives me hope for the LEGO Movies going forward. I'd imagine this movie will only really be made if TLM 2 does well. The original LEGO Batman movie only barely touched on a lot of interesting characters and concepts that I'd love to see explored in a future film.