Before comparing the guitars, I want to mention that A) The Sterling JP can be found in a satin black finish for $500 and B) an RG1451 Prestige can be found for $800.
With that out of the way, the main difference between these guitars, outside of the pickups (which you mentioned you're swapping), is the neck in each. If you're a guy who loves a smooth slim neck, go with the Prestige. If you're a fan of a bit thicker, unfinished maple neck, go with the Sterling. The other variables, such as headstock, body shape/wood (both are basswood though), machine heads, etc. are much less important than the general feel of the guitar, which starts at the neck. I will say though, as someone who has played both recently, the string tension is certainly better on the Prestige, as the Sterling felt a bit stiffer moving around the notes and bending freely.
Just my two cents mate.