I don't know where I've read this--probably in this thread--but the actress playing Koyomi had conflicting schedules so her role was reduced. And with Koyomi's story being the motivation behind both hero and villains, the story was forced to meander for a while. CMIIW though.
Production problems are always interesting to see, and managing productions for a show that lasts entire year sounds like a nightmare in this age, where new series are one or two cours at most. But they really need a year of toy commercial campaign to run.
I don't think Koyomi's role being reduced had anything to do with the story meandering, it just reduced her development and resulted in things like them always flashing back to the same couple of moments she shot outside to show she had bonded with Haruto in the final few episodes.
Wizard's story structure is pretty typical for shows produced by Utsunomiya, it's just he's mostly a Sentai producer (Shinkenger, Gokaiger, Toqger, Zyuohger, Lupinranger vs Patranger). Wizard suffered compared to them since due to only having two Riders compared to a full Sentai team there was even less they could do while the plot wasn't advancing.
Ultraman proves that they don't actually need an entire year, it only runs for 25 episodes per season and the toy sales are good.
Ultraman's toy sales in Japan are still bellow even current Sentai. It just makes more money outside of that, and only since last year, so a large part of it is just Sentai's sales falling more and more. Also, Bandai outright owns 49% of Ultraman while they only have a toy license for Sentai, so it's hard to tell where that money is coming from. You can see something similar (to a larger scale) with Gundam in Bandai's financials, where the overall group numbers also get a big boost compared to just the Japanese toy numbers, but it's yet another franchise that's owned by Bandai (and this one is actually fully owned).