well, right now, we need to focus on his enemies so we can then get to his final form.

also, I think side riders are better used when they don't have a direct involvement to the main character.
like, Date had no involvement with Eiji and I loved that, they were just 2 completely different people who had to work together.

A walking nuke is an interesting idea. His extinction form could have the ability to actually cause an extinction.

that could be the power of the extinct.

being able to turn objects or people into exctinct like creatures.

A main idea for Rider is "The Hero uses the powers of the Villains against them."

Ryotaro gets possessed by Imagin, Haruto gains his Magic from his own Phantom, Wataru employs the former King's Kivat partnership, Kenzaki harnesses the Joker's ability to seal Undead, Takumi uses Smart Brain's own tech to topple them etc.

How do the enemies of Paleo function to encorporate Amber Stones? What is their plan for them?

As a basic MOTW premise, I imagined The Extinct turning fossils into Kaijin. Perhaps every now and again re-animating an entire Dinosaur skeleton to do their bidding.

Nowadays Kamen Rider shows usually contains 3 themes: the theme of the Rider(s) (ie. Legend of Momotarou, vehicles, elementals, fruits), the theme of the Villains (ie. Constellations, fables, stained glass monsters), and then the theme of the plot which sometimes relate to the modus operandi of the villains (ie. Desire, hope, sacrifice). Maybe we can organize it in this fashion first to see how Paleo, the Extincts, and their goal/methods all connect.

Why stop there, let's make em also occationally turn people into fossils then use evil amber stones to turn their corpses into monsters

that could be good for later arcs, but probably not good for an entire series story.
like, OOO had Gamel turn people into medals which was kinda nightmare fuel, but I think it would make the series too dark if it was used through the entire thing.

I like the idea of people being forced to turn into monsters of the week, but not all the time.

That's an amazing idea, we have to do that for the kaijin.

but how would they procure of fossils in the first place?