This isn't a question about the pros/cons of Lightning/Visualforce, but is a question about how to build custom UI for the period of time (a year or many years?) where some users/orgs have Lightning Experience turned on and other users/orgs don't.
Is the answer that you have to implement the custom UI twice, once in Lightning and once in Visualforce? Or is there a better approach?
(I am thinking particularly about managed packages that in principle should work in all sorts of orgs, but the problem also applies to once-off code in an org if only some users have Lightning Experience turned on.)
The comment thread on the question below includes a link to Trailhead's Visualforce & Lightning Experience (Learn how to use Visualforce to customize your Lightning Experience) which looks like a good resource on how to get existing Visualforce to work in both classic and lightning environments. I'm getting the impression that building app UI that uses Lightning technology at all (client side MVC etc) will not be commercially rational (and there are certainly technical limitations too) for some time to come...