Number one is Tsuburaya's
Bio-Planet WoO from 2006. In my opinion it's the best thing they've made since the original
Ultra Q waaaaaaaay back in '66 and definitely the most satisfying of their series from the 90s onward. Very beautifully shot and with an expertly-crafted story.
And the second is another TPC show:
Ultraman Max (2005). Most people swear by
Ultraman Nexus but Max just does it for me a lot better. A lot of very talented people worked on this one and it really shows (not to knock the very talented people who worked on TPC's other great shows). Some of the episodes are quite simply some of the best the Ultra series has to offer and I'm constantly coming back to this show when I want to introduce people to Ultraman for the first time.
Then there's
Mikazuki (2000). Design-wise it's absolutely fantastic - Keita Amemiya is a Golden God in that respect. The reason it only makes third best, however, is I just don't find it as fulfilling as the other two and the pacing feels just a little off at times. It's still amazing, though, and the
Gekkoki pilot is one of my favorite characters ever.
