It all depends on your power, enclosure, how much room you have to work with, etc.
If you have the electrical and spacial capabilities, I'd go with the two E-15s. Assuming that they're both in optimal enclosures, the E-15s will probably end up out-performing the single SA-15 due to having double the cone area, and two motors running instead of 1. Again, it totally depends on the enclosure and electrical setup, but that's the route I'd go. If you have plenty of room to work with, I'd go with the E-15s. If you're crunched for space to the point where you're not going to be able to give the Es the room they need, I'd say the SA.
By the way - if you end up running the two Es, I'd invest in a larger amp.