Alicante-Elche airport accounted for over 10 million passengers in 2015. During the same year, numbers were down 2.5% at San Javier.
From our house, the two airports are about equidistant - it takes about 45 minutes to get to either. Given a choice though, I would fly from San Javier but there is a snag and that is the number of flights. Some carriers don't operate from San Javier in winter and those that do either charge more or fly at unsociable times.
Why do I prefer San Javier?
I prefer the journey there and the small size of the terminal. In summer, Alicante-Elche can be a nightmare from getting through security to picking up your baggage and even access to the airport by road.