Records from the 1990s = EPO
The biggest limiter on a road bike is wind resistance so you are right, that hasn't changed much. The biggest difference between a bike today and a 25 year old bike is weight (a marginal gain), ergonomics (STi/ergo shifting/11 speed), tires (lower rolling resistance), and aerodynamics. Aerodynamics though hasn't yet invaded every price point of road bike.
I'm going to say that I think a top of the line aero bike (Trek Madone) is quite a bit faster than a top of the line road bike from 25 years ago. It's probably not enough of a difference for a recreational rider but a 25 watt* difference at the pro level is huge.
*just pulling 25 watts out of the air
I have to disagree on some points, and agree on others. I personally believe that at least some, if not most pro riders nowadays are still "enhanced" in some sort of way. Thats just the nature of the business in professional sports... And you would think that modern bikes and better training methods + possible dope would shatter the old records, but really thats not the case. Certainly EPO and the best bikes help. But 90% of the story still comes down to the level of fitness and mental toughness, regardless of drugs or technology... Just my opinion.
And some things you mention are not exactly true. 25 years ago, it was mostly steel and in the 20lb range. Once alloy and carbon hit in the mid 90's, the pros were riding 15lb bikes.
And they also had STI shifters in the early to mid 90's. 7, 8, 9 speed. Honestly, once your 8 speed and above, your gear spacing is pretty good, especially when you run a straight block 12-23. 8 speed vs. 11 speed would never hold you back in practically any racing situation... I mean yeah, Ill take the 11 speed over the 8. But honestly Im not even thinking about it when Im riding. 8 speed is quite good enough...
As far as aerodynamics, I feel the riders back then didnt even think about it. You had guys doing TT's with no aero helmet, and aerobars attached to a normal road bike. They wore loose clothing that flapped in the wind. Aerodynamics has come a long way since! A huge part of that has been the clothing rather than the bike. The bike only creates a small amount of drag compared to the body.
I think where a modern bike would really shine is fast 20+ mph riding on a breakaway or solo effort, where aerodynamic wheels and frame would give some nice incremental gains that could add up to minutes over a long race. It wouldn't matter much if riding in a group, when your being sheltered...
On steep gradients, I doubt there is much difference assuming bike weight is the same.
And your right, it will be interesting to see the entry level bikes getting the trickle down technology. Aero frames would be nice, and modern groupsets are just way better than the old stuff. Again, not so much performance wise. But shift feel and ergonomics are way better nowadays. I much prefer a modern Tiagra vs. Dura Ace 7700 etc...