Why the heck is there only 6 ninjago sets for season 2. It lasted 13 episodes, the same as season 1, yet we get sets for only 6 of those 13 episodes. Where is the saw-blade and driller vehicle??? Where is the fully powered Overlord dragon? Why is there no final battle for Ninjago set? Why is there no Lighthouse set with Zane's father and the kraken monster thing???? And finally, WHERE IN THE HECK is the Stone Army Tomb!?!?!!?!?!? There are sooooo many more sets that Lego could have created for season 2, yet they failed to capitalize on those opportunities.
Believe me, my friend, I feel your pain. However, there's a couple things you need to be aware of:
1. Ninjago, like many Lego properties that aren't licensed, was originally intended only as a three-year theme. As such, those six sets were going to be the last ones we got. However, the theme proved unexpectedly and overwhelmingly popular, which prompted them to continue the theme and it's accompanying TV series.
2. The TV series is derived from whatever sets Lego comes out with; Lego doesn't create sets based on the TV series, unless I'm utterly misinformed about the process. As a result, the show's creative team includes the actual sets as best they can but then implements a lot of their own ideas, which typically only see life as fan-made MOCs. Season 2 was neither the first nor the last season where this occurred: several season one creatures and characters have yet to appear in physical sets, and the Overlord Dragon has companions in nonphysicality in the forms of The Preeminent from season 5 and the Colossi that's apparently showing up in season 8, among others.
Believe me, I'd love to see Garmadon's mech from season 2 as a set, along with the Overlord Dragon and various others you mentioned. However, it does come back to the fact that many of those elements were things the Hageman Brothers and other creatives derived from the sets, rather than Lego creating sets based on the scripts the showrunners came up with.