I'm at work and can't look at save yet, but here's a couple guesses to help see what you were looking at.
1: SE - You can check the message log to see if he built a few key wonders that help with SE, especially Pyramids for early representation is the biggest one. (+3

per specialist makes the SE better in early game). It also raises the happy cap by +3 for his top five cities (which is a fifteen population point advantage that works wonders on the low-happy-cap levels ~monarch and up~). The great engineer(s) you can get from adding a forge to the Pyramid city can help build the wonders in 2 below...
2: Maybe have Parthenon and National Epic placed in same city for massive great person bonus to help with 3...
3: He could have dumped tons of great scientists in a single city with that academy and and great library (and later Oxford University) for that massive science city (by mid game if you aren't pulling in 100+

per turn in that city you didn't focus on SE hard enough).
4: Hmm, multiplayer. Was it two player or FFA? If there were plenty of AI around, maybe he traded with them more. Once the AI has all the techs you have and more, it's hard for you to have a tech to trade with, especially if he was trading with them and leaving you out of the loop. You won't necessarily need a Specialist Economy for that.
That's all I can think of without looking at the game.