Alfalfa has a lot more of bunch of different nutrients. Protein is a big one. But Alfalfa also has high calcium which is great for growing baby bones but an adult can't use all that calcium and it often ends up as 'bladder sludge' which is not a good thing. Alfalfa also has a lot of calories and it's easier for a bunny on Alfalfa to get chubby (versus feeding the same amount of Timothy).
Timothy (and other grass hays)has nutrients, but it is a lot less in most areas meaning the rabbit is not getting an over abundance of calcium and calories that it doesn't need.