The main difference as I see it is that they were aiming for a different market...
The original CE's were a lot more 'expensive' relatively speaking and you could save yourself a few hundred bucks by opting for a CE over a core - not a big saving because the only real difference was the neck material and the way it was attached to the body. Perhaps it stopped selling in sufficient numbers due to the fact that you could pick up a 'Core' Cu24 for around the same price or less (sales, used etc).
When PRS introduced the S2, a way of reducing their 'costs' and therefore reduce the price of US made PRS guitars at about 1/3rd of the price, the success of that enabled them to target a 'new' audience - one that wanted something a 'bit more' premium with US made Pups, but still not as 'high-end' as a core which commands a 'premium' price range. To offer a US made Bolt-On neck PRS that isn't a couple of hundred less than a Core and have it compete 'directly' with their Core instruments, they had to reduce 'costs' - something they had experience of with their S2 range.
There are some that will claim a scarf neck joint doesn't affect the playability or tone, having steel instead of brass (or other materials) may not sound the same, but not necessarily better/worse, more/less premium - a cheaper manufacturing process no doubt. Some prefer the shallower carve top too as they find the edge on the Violin carve digs in to their arm when playing, Some may argue that the Pups are 'better' today than the pups PRS were making pre-2008 and whatever other 'changes' PRS has implemented as 'improvements' over what came before - like Phase 3 tuners for example. There are others who swear that the older ones are superior because they were 'core' instruments that were [almost] as expensive. Save a small amount by having a bolt-on...
Anyway, my point is that the newer Bolt-On's are not targeting the same market. These are aimed at those that either want a 'Bolt-on' specifically for its more 'snappy', more attack like feel and playability or those that want a Custom 24 with US Pups but can't afford or justify spending over 1k more for a 'set-neck' Core version. The 'new' bolt-on range is aiming for a different price-point, a different 'tier' than older ones...
At the end of the day, you have to accept what the used market has, whatever condition, colours, modifications etc and these are only likely to get more difficult to find one. On the other hand, the new ones will let you choose what colour, what condition etc as they are still being produced - I assume with the Nitro over CAB finish and TCI processed pick-ups...
I am NOT saying pre 2008 CE's were better/worse than the most recent CE24's, just that they are not necessarily targeting the same market today. They are, as originally pointed out, 'different'. The older style is no longer available so you have much more limited choice and availability. Cost too maybe a factor as some can be as expensive, if not more so than buying a 'new' CE24 in your prefered colour and of course, in 'brand new' condition too. Is a 1985 Cu24 the 'same' as a 2022 Cu24? NO!! but that's how things have 'evolved'. If you 'prefer' the older ones with Brazilian Rosewood boards, shorter heel, rotary and sweet switch, different Pups, wingnut tuners, different bridge, single action truss rods etc, then you have to buy 'old' - same as if you prefer the 'older' CE's too...
It's more important to get an instrument that works for you, regardless of where it was made, when it was made, how it was made etc and inspires you to pick it up and play it. I don't think there are 'many' guitars that can compete with the 'new' CE's at their Price Point but then they aren't in the same Price bracket as the Cores like they once were.. The difference in price between a CE and Core Cu24 back then would be like paying to upgrade from Vintage tuners to Phase 3 Locking tuners on the McCarty range, now you could buy a CE and S2 (or at least an SE) for the price of a core - that's put it in a different price tier and competing in a different market so I think its unfair to compare when they aren't really in competition and were built for a different market and that price difference also reflects that - like the SE range, and then the S2 range later on, PRS had a quite a big price 'gap' between S2 and Core which has now been 'filled' by their Bolt-on range - which now also includes the Silver Sky, Fiore and Dusty Waring models too. Instead of being a 'slightly' cheaper Core, the CE24 is now a more 'premium' S2 line and PRS often include their Bolt-on production numbers in with the S2's - Make 45-50 Core a day and 45-50 S2's (which includes Bolt-ons as they have the same Neck making procedure) and I assume, a similar thickness Maple cap too...
In conclusion, yes there are differences and reasons why too but the only CE you can buy 'new' today is the newer version and you have to get 'lucky' to find an older 'used' CE in the colour, condition, price point etc you want (or willing to tolerate - I couldn't tolerate a blue guitar regardless of everything else) but if you do find one, then you have a decision to make before someone else snaps it up...
