The only reason we even have this mess is likely due to Kobayashi not liking to handle things that contain other people's characters for some strange reason. Well, that and 'cuz post-Agito-Inoue wrote Nobunaga's Greed.
Really, I'd blame the main producer, Naomi Takebe. I don't think it's the script writer who decides if they're going to tie in a movie with a tv show. They shouldn't have enough power for that.
Even if Kobayashi didn't want to make tie in episodes with someone else's work, Naomi could just have gotten one of the other script writers to make the tie in. However, it's pretty obvious she just had no interest in tie ins with the movies. Even episodes 999 and 1000, not written by Kobayashi, ended up just used to promote the anniversary movie, rather than actually having direct story connections with it.
On the opposite side, looking back at Double, the episodes which had Movie Wars 2010 tie in scenes were written by Keiichi Hasegawa. The first episode with a Double Forever tie in was done by Keiichi too, but the second one, with the destroyed Fuuto Tower and the later OOO tie in scene were written by Riku Sanjo. So, in Double, different script writers still wrote tie ins, while in OOO, none of the script writers have done tie ins (and it has had 3 so far, Kobayashi isn't the only one).
I think producers are the main force behind those, not just the script writers themselves.
* Ryuki vs Agito
* Climax Deka
* Decade Shinkenger arc
and so on.
I don't think Ryuki vs Agito or any of the Den-O crossovers are good examples... The guest series are basically... guests, without much screen time or focus. Most of the time, they could be erased from the script without changing anything. Also, Kobayashi did write both sides of the Decade/Shinkenger story. Kobayashi has shown she isn't very confortable with crossovers, but I don't think that explains the lack of tie ins of OOO with any of the movies produced up to now that featured other Riders too. It's not like writing tie ins would need the characters from those series popping up in OOO anyway.
Regarding which one is the "main" OOO... It's kind of funny. Yes, the tv series one should be the main one, but what happens if the rumors of Double's producer returning next year are real, and we get some straight references to Double and even OOO? The OOO series would be the one shoved out of continuity, not the OOO in Double's crossovers.
On the other hand, if there's some continuity drawn by a later show, I guess you could also look at the OOO in Movie Wars Core like one does to Kamen Rider Vs Shocker (the first proper Rider movie of the original show). Yes, it can't really fit anywhere (Sakurajima Rider 1 with his own transformation, skelleton unifrom Shocker troops already present, but Hayato still hasn't left Japan, etc) but it is in continuity anyway (because the villain of that movie shows up later in the tv show and Hongo recognizes him). If you follow comics, that happens once in a while there too.
