I kinda get what you're saying, but I'm not sure that comparison holds up.
The rough-around-the-edges P.I. has been a popular archetype dating all the way back to the black & white days of detective stories.
And while it's true that Yagami is a bit more refined and slick due to the nature of his character and education, he's not exactly a secret intelligence agent type character either.
While I believe we'll get a third game and have at least some confidence it'll star Yagami, if anything The Kaito Files IMO proved Kaito can work as a main protagonist, even if he approaches situations differently and tends to have other means of getting results.
I can somewhat relate to the concerns over Kiryu comparisons, but I think Kaito is different enough to stand on his own. Besides, people generally seem to want more Kiryu content and this would - in a sense - be a fresh way to do it.