I agree with the OP to some extent; mainly, recognizing that a 3:59 in the 50's/60's was intrinsically superior to the same time on modern tracks.
My feeling is that the invention of modern tracks wasn't intended as some type of con to let athletes run faster at the same effort; there are other factors that make them superior (such as their all-weather properties, as mentioned by another poster).
I hear the complaint about tracks nowadays being "tuned", but i was under the impression that there are strict limits on the hardness/softness of tracks nowadays. If that is accurate, the benefit of modern tracks could essentially be standardized and frozen in time.
So I think you could say that while a 3:59 today is not the same as a 3:59 in 1954, at least it is pretty much the same as a 3:59 in, say, 1985 (i.e. we say correctly that Bannister, Ryun, etc would have run faster, but we don't generally say Coe and Cram would have run so much faster on modern tracks)...that is, until the "new shoes" came along. Maybe the new technology hasn't really had much effect on middle distance running yet, but it seems like just a matter of time. That's why I'd like to see it outlawed. Because while we can't realistically duplicate the conditions face by Nurmi, Zatopek, Bannister, etc (and wouldn't realistically want to), we had, until recently, settled into a nice sort of standard for how tracks and shoes would be, and it was easy to imagine them always being that way for the foreseeable future.
And I think that is a good goal for athletics: improvements in training, nutrition, psychology, etc, are all great, but keep the actual sport itself standardized, so that we can compare times across eras and extract some meaning from it.