The basic design of Fender, Gibson, and other brand name solid body electric guitars hasn't changed in 50 years or more. They were mass produced in the beginning (that's what they were designed for) and they are mass produced now. The only thing that has changed is (in some cases) pup design, and old tools have been replaced with new ones (generally more precise and higher quality). The woods that are most often used aren't that much harder to get than they used to be, just more expensive (what isn't?). Sure, there is variation, some guitars are better than others; some times the assembly process happens to hit the right body with the right neck and the right pups, it happens in any mass production operation. Sure some of those old guitars are some of the greatest guitars ever built. But, some of the best guitars ever built came off the line yesterday, too.
Your "average" new guitar has nothing on the "average" 50's/60's." You can't get a Fender w/ a decent "comparable" vintage type Nitro finish without going to the Custom Shop. Even my $2k AVRI Strat has a "meh" finish on it compared to my old Jag. Woods and playability on Fenders - sure - but that great "feel" that comes with a good Nitro finish... tough to find - hell, impossible to find in the regular Fender import or USA lines - and you pay a whole lot for what was once "the norm" through the Custom Shop.
As for Gibson - they've kept the basic shape but that is about it - unless you go to the Custom shop. Short neck tenons, giant chambers to reduce weight in an effort to combat the crappy dense wood they use now... Even the Custom Shop "reissues" have a ton of plasticiser in the finish. I own one - and it is "a good one" - yet it has nothing on my '69 Les Paul. Better wood? Who knows - but there is no question that one is much nicer than the other - which is the best that Gibson has to offer today. The light weight old growth Honduras mahogany can be found today in limited quantities, but Gibson sure isn't using it on their "regular" production models.
There is a difference - I'm not just talking out of my arse. Maybe some people prefer the feel of Poly Armor under their fingers, but it just doesn't do it for me.