Guy, I feel like I came to the end almost entirely to respond to your original post which was actually uncharacteristically REALLY REALLY LONG for you >.< Hell, it looks like some of my G+ posts >.<
Since the main topic is really drowned out here by page 59, as you pointed out, I wanted to touch on the first part you said, which actually, surprisingly, no one really commented on in the first few pages.
I'm something of a firm believer that if we ever REALLY get back into a Star Trek series we need some kind of mega technology update. The Doctor (and to a lesser extent Data) were both based on our comparatively limited understanding of AI development back during the 80s and 90s. Back then, we envisioned AIs to essentially be a cluster of nested IF and OR statements
while today, if we were going to truly tackle a character like The Doctor, we by all rights should be basing it's AI on theorteical concepts of quatum computing as we understand it today.
Putting that a little more into perspective; the big difference between us and computers is if you give computers a problem they work out the solutions based on all its programmed variables each time it completes the operation. The human brain on the other hand recreates the process each and every time it does an operation known or unknown and each time it does that the human brain allows for recently assimilated knowledge to become factored in to the process allowing you to either perceive shortcuts, easier ways of doing things, more efficient ways of doing things or that ilk.
As we understand computers today, an artificial life form would almost certainly use quantum processing that mimics biological brains versus binary processes which are rigid and systematic.
That being said, I will point out that you're absolutely right, as we understand computer science today compared to when the series was made, we have no right calling The Doctor anything more then a toaster based on what we know about it's design. >.<
Oddly enough, we can tug on far too many other areas of Star Trek >.< Its a little scary when you stop to think for a second how dated Star Trek is because of some of our advancements yet our advancements have been at a proverbial crawl the last decade or so >.<