Henrye,
No need to be intimidated. Its a great topic, and philosophical at that, worthy of the board.
As a modern architect, I like to think that your premise is largely correct - modern courses should be and are better. On the other hand, visit any of our websites, and 99 out of 100 architects agree, we are "paying homage to MacKenzie" or whatever. Imitation may be the sincerest form of flattery, but it is still imitation! We must believe the art form was basically perfected in the Golden Age, (at least for American inland courses) and we are simply applying those principals. Of course, CB MacDonald said that in 1900 or so!
IThe top courses of any era are more than functional - they are works of art, and no generation has the monoply on artistic talent. I feel the top courses of each era compare favorably. In fact, the modern classics really are different mostly in application of technology that couldn't be applied before - Artificial dunes at Whistling Straights, Waterfalls in the Desert, Golf courses on hilly ground owing to carts and cart paths, etc.
I believe architects of all ages design for their clients wishes and target audience. As Adam suggests, there is more emphasis now on playability for all than there may have been when the audience was almost exclusively rich white men. Most courses are built on sites that don't offer everything - over different eras, different design characteristics were emphasized, and in some areas, you give a little (like close green to tee walks, and thrilling tee shot carries) and get a little (like spectacular vistas, or more safety, faster rounds and playability by all).
Everyone is entitled to their favorites, and even their own bias' in how they choose their favorites. Comparing purely objectively is not so simple, especially when you consider each course is built for a specific purpose, which is not always to be a top 100 course.
I would wager that the broad middle of today's courses are much, much better. There are more talented designers today than ever before. Lastly, I think human nature pushes standards higher generally, meaning that more courses today have built in maintenance and design quality, etc. that classic courses took years to implement, like even moderate irrigation, and that means generally better courses across the board.
But, a classic is a classic.....