@Dancing Frog is the 513-wiseman.
I'm owner of a core 513 MT (with a modification regarding electric parts: no printed circuit board (PCB), but hand-wiring).
It's right that there have been a few improvements along the "life time circle".
The first models came serial with BRW neck, Phase II tuners and compensated 513 nuts, PCB (513 RW). 2007 the "classic" core model detached the RW model: mahogany neck, rosewood fretboard and than the above mentioned specs.
2010 (25th Anniversary) a limited run of swamp ash bodied 513 had been launched.
2011 the core model has been named 513 MT (maple top), as a connecting part with the older versions they came along with PCB, but over the year a few parts were detached: Phase III instead Phase II tuners, new PRS nut instead of the 513 nut.
Did the PCBs had a few revisions since first announcement of the 513 in 2004, 2014 PRS decided to rip off the PCB and to braze connection cables among all electric parts for delivering the best possible and transparent sound.
Currently improvements are - my pov - only due cosmetical issues.
That all said: Dancing Frog is capable to say everything about tonal differences within his own collection.
My experiences are more limited: I played in 2001 or 2002 a CU24, owned end of November 2011 my 513 MT, got it modified in 2014. Compared it with three other 513 (one RW, one MT from 2011, one MT from 2013) at one date in late summer 2014.
Unplugged I noticed differences in the sound of the RW to the MTs, plugged there've been little differences switching through all modes and pup combinations. But I do not relate that to wood specs but to different adjustments of pups heights.
At that date I had the opportunity to play Paul's former "back-up" P's G.
Recently I played a PS DGT at a GC.
Yes, I only have got one 513 (and I'm biased, because I'm very convinced by that tonal versatility), but sound-wise I was never disappointed compare it to other even more expensive PRSi.
I underline everything what my dear friend Nabil aka
@g.wizz stated, but I'll push his words to a climax: Once you've endeavoured all the beneficiaries a 513 provides you need not to chase other guitars: nasty dirty sounds, chiming sounds, powerfull voicings in one - and good looking - PRS.