Why is the Alekhine's Defence all that great? For example, let's say that white plays e4, and then black plays Nf6. White could just counter with Nc3, which would both protect the e4 pawn, develop a knight, and not overextend white's boundaries by moving the pawn forward. I don't really see how it's that great.

It's never that easy.

1. e4 Nf6 2. Nc3 e5 and white is playing the Vienna game, I don't mind playing it from the black side.
1. e4 Nf6 2. Nc3 d5 and we're in the Scandinavian variation, I don't believe in 3. e5 because 3. ... d4.
1. e4 Nf6 2. Nc3 d6 we have a Pirc here, don't mind playing that either.

Bottom line is black can choose whatever system he wants.

I just made a thread about this same opneing, except I'm interested in hearing people's thoughts on playing this position as white. Check out my thread and tell me what you think.