Precocious is certainly one word for him. In the S1 behind the scenes extra, Andrew-Lee said that the producers/writers told him that Connor was supposed to be a genius, so that would go well with him actually developing all these skills, even from a young age.

I hadn't actually thought of those points about the physics of the anomalies and such with the magnetic field, but you're right. In some ad-hoc way he's already testing and analysing the anomalies right from the start, without all the scientific might of the ARC behind him (and I really wish they would actually show the team analysing the hell out of the bloody anomalies rather than just reacting to the creatures - they're rips in the fabric of time, for gods' sake! Analyse them and find out what they are and how they work!!!! Sorry, mini-rant over).

I personally have no trouble believing the character had those skills all along, I'm just not certain that the writers of the show knew he had them! Not until the did the time shift into S2 and they decided to make a few changes. Does that make sense?

And of course I'm completely with you about wanting more of Connor generally.