Interesting, but there's not a lot going on so far. Backstory is nice, but I like to piece together most of the obvious parts.
He's oddly savant for a six year old, despite being a time Lord it's not an excuse for that much intelligence. Your character at this point is a model Gary Stu, though it is still possible to save him, since we technically haven't seen him in action hardly at all. I expect at least a little ineptitude when it comes to interacting with your average pony since (according to his story) he never got out or had friends. Now, we're not saying you should model him after, say, Twilight, just don't make him infallible. A story in which the main character is perfect is boring, and hopefully you don't walk down that path.
Keep going! ;)

5380670 Trust me, he has many flaws one of which was his obvious need for attention and to be seen in a cool demeanor. Other quirks will be made visible as soon as he interacts with more ponies(his age). Also, you are a mind reader With the Twilight thing, i mean.

5383480 We have been accused of mind reading before, but alas, we do not have such facilities available at my disposal.
I do however make it a background practice to evaluate and analyze potential time streams and alternative divergence paths.

I like this so far.

5410260 Thank you