I currently have a Sterling guitar (not a Petrucci but the EVH inspired AX40), a PRS 24 SE, and an OLP Petrucci (precursor to the Sterling line).
Bottom line Sterling guitars are better than great guitars (not just saying that because I endorse them, either). I've only played a JP100 at Guitar Center and it was light years better than my OLP Petrucci in terms of feel. The Sterling version has a much better tremolo that is closer to the EBMM version.
The PRS Cu24 SE is a great guitar that I just can't let go for some reason. I'm not a fan of 24 fret guitars, nor do I care for finished necks, but damn if it doesn't play well. Easy to play, great tremolo system, comfortable to sit with. I also have an SE245 that I use regularly as well. I typically have my PRS SE guitars for jamming at home, while the Sterling is my main gig and practice axe.
First thing I did to both of my PRS guitars was change the nut. Away with the plastic nut and drop in a TusqXL. Cheap and relatively easy to do yourself. Aside from that not much you need to do to those guitars to make them reliable other than straplocks.
Honestly, Sterling and PRS SE guitars both get my vote for best bang for the buck guitars. I have owned my AX40 for 4 years now and has been through thick and thin lol. New you'd probably save a little coin going with the Sterling, but used there are more PRS SE guitars to choose from, and can be found cheap. I bought my 25th Anniversary Cu24 SE for $250 off Craigslist, with ca
But honestly if it's a choice between the Petrucci and Cu24 SE, I'd go with the Petrucci. I say that mainly because of the finish on the neck. Doesn't have a gloss finish that likes to stick to skin - it's much faster to play if that sort of thing matters to you.