Long post incoming! But you asked for some thoughts, so here's the low-down:
You were comparing a Gibson USA production guitar made in Nashville vs. a Historic 1958 Reissue made in Gibson's custom shop in Memphis. There are quite a few differences. Armann's comparison of a 1550 with a J Custom is pretty apt.
The Studio Deluxe is going to have swiss cheese holes in the mahogany back under the maple cap. This is to get the weight down to a more reasonable 8 or 9 pounds. You will be lucky if that mahogany back is a 2 piece. It could be 3 or 4. Some studios are even more.
The Historic reissue is going to be one single piece of mahogany selected specifically for weight. Gibson tries to aim for a total weight of around 9 pounds for R7s and R8s, and around 8 pounds for R9s and R0s. The overall quality of the wood is going to be higher.
Then there's the neck tenon. Go read the TGP or any Les Paul forum and you'll see endless debate about this. Truthfully, I don't think it in of itself has much bearing on the tone, but it does indeed effect the angle the neck is to the body. A long tenon will keep the neck at the proper angle until the glue dries. This could very well effect the sound. Long tenons are found only in Historics as it is much cheaper to have a short tenon, which is what you'll find in basically every Gibson USA guitar.
A few other points:
- The Gibson USA is a production guitar made in a factory. The Historic is going to have more one-on-one time with a luthier. It is NOT completely hand-built, but a lot more TLC is going to go into the fit and finish. Fewer people who are better paid.
- The Historic does have better electronics, specifically the pots. However, they do NOT have actual bumblebee capacitors, despite what the tag says. Those bumblebees you see under the plate are not real paper and oil capacitors. They're just colored to look like them.
No worries, if you want real ones there's an entire cottage industry out there that strives to get a Historic even closer to the real thing.
- Pickups. The pickups on the Historic are going to be Burstbucker 2 or 3s, perhaps '57 classics. These are PAF repros that are a bit sweeter than the 490 and Burstbucker Pro on the Studio Deluxe.
- Overall Historic quality is going to be much higher, but that doesn't mean that a $3000 R8 or $5000 R9 is going to be flawless. Les Pauls are a luthier's guitar, not a wooden plank with a neck bolted on. Between the set neck, binding, carved top, etc. they're harder to "get right". A lot of the flaws you see people complain about were actually present on the originals too. You should still run the racks and be observant of the fit and finish or...
- Buy used from someone who did! A used R8 is usually the same prices a new production Standard or Traditional. Keep your eyes peeled and you can usually find a good deal.
Funny you mention the Studio Deluxe, because I bought one.
Specifically because it is less like a Studio and more like a Traditional or Standard sans binding. It does the Les Paul thing and it's a good contrast to my Jem for recording. You can typically recoupe most of what you paid when you sell a Gibson, so I might trade-up to an R8 in the near future. In any case, I'm going to splurge on some Peter Green boutique pickups for it.
Keep in mind I played LOTS of Les Pauls before finally buying the Deluxe, including Historics. The Historics were better, but not $1500 - $3500 better. The Deluxe was THE best amoung the Gibson USAs I played. Use your ears, not your eyes.