Why go through iMessage when you want a direct connection? I think it's just a matter of Apple getting it right and figuring out how to ensure a good experience, yet allowing 3rd party apps to use Siri.

Because using messages you already have access to a lot Siri's understanding. 3rd party access could be very problematic if you consider that Siri would have to understand also several way to say the same things, otherwise it would become just simple keyword recognition.