Why did lego stop the Ninjago Spinjitzu Flyer and switch to the Ninjago Spinjitzu Spinner?
The flyers were released in 2015, 2 years is an average production run for LEGO sets. Note that spinners have been released before, in 2011 and 2012 with expansion packs like cards and weapons.

I think the most likely reason that the flyers were discontinued is that LEGO did not see enough marketing potential in a second wave.

As to being more "fun", that is entirely subjective. These flying plastic rings were around in my childhood as well and I hated them.
To me they seem now old fashioned compared to the myriads of flying drone toys that are available today.

Update: Apparently, it was a bit premature to state that the flyers line of ninjago had ended: https://brickset.com/sets/theme-Ninjago/subtheme-Dragon-Masters