I think Kelly was the best candidate for the job. He had the best record, and he was the candidate with the strongest leadership qualities.
The only reason why Jen was there was because Jen was a better defender/self promoter, and would make for a better TV finale. That's why he fired the Kevin with Sandy. Kevin was a stronger leader than Jen was, but between Kevin and Kelly, it would be too clear who the winner should be.
Trump knew he was going to hire Kelly weeks before he did. Jen was only there to obfuscate the decision and draw interest to the final episode.