I can't be for certain ... but after reading and watching TONS of stuff on everything Jurassic Park ... I can recall Crichton saying that he developed the Ian Malcolm character after himself. That he had no plans to do a sequel. That Spielberg repeatedly encouraged him to write a sequel during the pre-production/production/post-production of Jurassic Park the film.
He of course decided to go ahead and write the sequel ... but he had to write 'himself' back into the book somehow.
It didn't hurt that the cast Goldblum as Malcolm ... making Malcolm infinitely more cool that Crichton could ever hope to be.
And he was a box office draw where as Sam Neill wasn't.
So a combination of money, ego, and Spielbergian influence brought him back.