So the USS Kelvin is technically a Prime timeline ship, since it was before the Narada incursion. The Narada was far bigger than the Kelvin. Far, FAR bigger. It seems only logical (sorry, I couldn't help it) that Starfleet would consider this going forward. Those in charge of the fleet likely decided they couldn't be caught so unawares in the future and started designing bigger ships. To me, it only makes sense that the ships are getting bigger earlier in the Kelvin timeline. As someone mentioned earlier, look at Yorktown! Holy cow! If they can build something that big, why not build bigger starships?
Back in the Prime timeline, it's possible that as they moved forward on designs for ships, there may not have been a need to make the ships bigger right away. So when they designed Constitution-class ships, they made them a little smaller than the Kelvin.