James,
Thanks for taking the time to respond thoroughly. The key, for me, is about making this an option rather than a requirement. I simply find it hard to believe that Jon B would reverse the entire trend of his company, and require a cloud-based program. Your final interpretation of what he is saying seems cynical to me; Jon B has known all along that it is a challenge to deal with all of this disparate hardware, cobbled together networks, and relatively IT-challenged docs. Sure, a cloud solution would be far easier for him and for the company, but I don't believe that he will insist on one.
What I want to remind you (and the other technically minded people here) is that the average physician is feeling maximally stressed by the concept of going to an EMR. Despite pretty major incentives, many have held off. Sure, many have done it...and many of those are tremendously unhappy and are looking to change. Most small practice docs don't employee a Bert or Indy...they don't even know of one. Their ideal is to order a product and start using it the next week, with minimal disruption as they continue practicing medicine. To me, just as AC needs a PM to stay competitive, they also need a more effortless solution, and that means one that is cloud-based.
I think the choice MUST involve picking a provider that you can trust. You could work with some faceless corporation that puts you at the bottom of the pecking order and subject to all of the indignities you describe. (Not to mention that they could get rich selling your data a la Practice Fusion). If it were me, I would look for someone I trusted (like Indy) to set this up so that I could feel confident that there was a commitment to ME as a small but important customer. Someone who I could trust to keep an eye on my interests and MY data. Not some faceless, shapeless "cloud", but a person who makes my practice of medicine easier.