Well i think we mostly think that a season of an anime series is from the start of the anime to the end. In this case we see that SMC start from the start of Dark Kingdom(Obviously) and end at the end of Black Moon so we counted it as one season but Japan think a season of an anime is they broadcast in three month. SMC Dark Kingdom Arc broadcast exactly in Winter Season 2014 and Black Moon Arc start in the first week of Spring Season 2015. So to Toei it like season two Black Moon air imediately in the next Season
About OP i think its Toei's habit: Conan, One Piece,... change OP very much but DBS using one OP(only changing featured character in OP) nearly two year -.-!
I think it also has more to do with the story itself, I mean, season 1 was clearly focused on the 'Dark Kingdom' arc from the manga, while S2 was focused on a completely different story arc and focused on the 'Black Moon' arc from the manga, so it's divided into 2 separate seasons. They did the same thing with the classic 90s anime too, even though each season of the 90s anime was much longer than Crystal (each season of the 90s anime lasted for about 1 year), but the first season was completely focused on the Dark Kingdom arc too, then the second season 'R was mainly about the Black Moon arc. So I think the 'seasons' are probably more determined by each story arc from the manga, with 1 season focusing on 1 particular story arc from the manga.
But seasons 1 and 2 vs season III is very unbalanced:
1 & 2 use the same opening song with basically the same opening visual sequence (save a few minor differences)
III uses three different versions of a new opening song with a different opening visual sequence that slightly changed over the course of the season.
1 & 2 use the same ending song and visual sequence.
III had three completely different ending songs and visual sequences.
1 & 2 use the same eyecatches.
III had its own eyecatches.
1 & 2 had an "A suivre" TBC card at the end of each episode. III did not.
Season III was clearly marketed as such, with the use of the Season III subtitle. "Season 2" (aka Phase 2, the Black Moon arc, etc) had no such obvious subtitle/distinction.
The reason people are a bit confused about Crystal's "seasons" is that the first 26 episodes were formatted as one unit whereas Season III has been formatted in a very different way.
I think this might be because the first 2 seasons were both directed by Munehisa Sakai, but he was later replaced by Chiaki Kon for S3 onwards and so many things changed in S3, the styles and artwork and direction etc all changed under the new direction by Chiaki. Every director has his/her own different styles and opinions and preferences and different ways of doing things, so with the change of director for S3, many changes were bound to be made.