This isn't about how to capture enemy universities or even why. It is about what happens when you do (or how come I get free technology sometimes and not others?). In the MK help file, the only thing said on the topic is "Remember to protect your Universities since others may invade the city and get that technology for free!" (I was able to find the "Buying a University" help by looking for Universit in the Index. I couldn't find it through the Contents). Obviously, this does not say everything. What follows is part common knowledge and partly my own theory of how it works.
When you capture an enemy university, the game checks to see if you have a higher or equal level of technology in the original field of the university (as compared to that enemy). If you do not, then you are awarded one level of technology in that field (ie. if you had up to commando, you would get the Striker but not the Tiger). If you do have a higher level, then it checks the other fields and applies the same comparison. For example, if both players have up to the Patriot in Ground Technology and up to the Hercules in Air Technology, then neither player would be able to steal more advanced technology from their opponent. But if one of the players had the Artillery technology as well, then no matter what kind of university the other player stole he would get the only technology he didn't have yet (ie. the Artillery). If your opponent has all the naval technologies and you have none, but the rest of your technology is the same, you will steal their naval technologies whenever you capture any kind of university from them.
As I said before, this is only my theory on the matter. I could be wrong. However, it is born out by the results I have achieved so far.