Neck-thru versus bolt-on is a taste thing, primarily. They sound different, but not dramatically so.
The SR500 has a 3-band EQ as well, but the SR500 pickups + preamp are darker and fatter in character to my ears than the Stiletto pickups + preamp, which are clearer and more balanced. You can compensate for either somewhat by turning knobs, but I (and this is a very personal thing) prefer the Stiletto.
The SR500 will have a smaller neck profile than the Stiletto as well, although both are quite comfortable.