Your point about design being cyclical is entirely valid.
As an example, go to the local appliance store (or Best Buy or Search or Home Depot or whatever). Look at what all your new appliances look like.
They're almost all brushed stainless or something in that vein, aren't they? That's the "artistic" style element that people are calling "modern" today.
Now, go back and look at the style of appliances which were being sold in the late 1940s and into the 1950s. And what do you see? You see stuff which is almost INDISTINGUISHABLE from the current design styles!
Of course, the underlying technology has changed, in some cases with minor tweaking and in some cases in fairly dramatic ways (glass-top radiant stoves, for instance... that's an actually innovation and a damned good one at that!). But the STYLE is simply... well... a matter of artistic taste, not functional design.
I'm glad to see that this topic is finally getting some rational discussion... to those of you who've attempted to seriously answer (instead of what's always happened in the past... ie, just more unsupported "well if you don't' get it, you're part of the problem with Star Trek" stuff!).
I don't necessarily agree with everything being said... as a major "form follows function" sort of guy, and a fan of the "modular" design which MJ had in his mind when he laid things out... I've never had any problem seeing a reasonable design looking at the TOS E. I've also never had any problem with any of the Probert work on the TMP E... though I've never particularly liked the engine nacelles we see there (a lot of detail, but most if it seeming to be there to "look cool" rather than to serve any rational function... tiered skin structure and so forth... FINS, for crying out loud... and so forth!).
You're right, Dennis, about being able to tell which era different ships came from... but I'd argue that it's not so much a matter of being in line with the prevalent OTHER design philosophies of the time.
If the design of the 1701 had been made with 1960s aviation ideals in place... it would have been bare metal in appearance and more "dart-like," or perhaps with a big "scoop" up-front. You can't draw any parallel with 1960s naval design... because naval design still looks almost identical today. However, there are STRONG influences of naval vessel design which are very evident in the 1701 design. You can't draw any parallel with space vessel design, either to contemporary real spacecraft or 1960's era space vessel concepts. The ship doesn't resemble either... which makes sense, since none of our current past or current spacecraft designs really have ANYTHING to do with the sort of ship Trek is trying to present... it's like comparing a log raft to the Q.E.2.
Then, you can look at "popular" styles. This is most commonly reflected in automobile designs. Well, cars in the 1950s and 1960s tended to have lots of fins, bulges, and so forth which provided no function except to "look cool." (Sort of the like the 1701-refit's engines, really.) Today we've got a "retro" design chic which gives us some of that, again... but with a subtly different spin (Dennis' car example is a great example of that... two cars which are very similar on first glance but aren't quite identical). But the things that these cars share in common are the "non-functional fins and bulges" aspects... under the hood, they're very much different.
For me... the idea of engine nacelles being generally cylindrical makes perfect sense. The idea of having them be mounted at a distance from the hull makes perfect sense. The idea of not having lots of nooks and crannies (aka "stress concentrators") in the exterior of each principle section makes perfect sense. The idea of having two separate hull sections makes perfect sense as well. And the logic behind having as little on the outside (read "in a hostile environment") of the ship as possible is, I think, unassailable.
If I were going back and redesigning the 1701 with MJ back in the 1960s, the only real changes I'd have suggested would be to increase the design robustness of the separate section interconnections. That is... change the engine pylon and primary-secondary-dorsal elements.
If I were doing that, I would NOT go with a TMP-style "aft-swept" engine pylon... which is really weaker than a similar-mass rectangular one like seen on the TOS ship! What I WOULD do is make the pylons about two and a half times longer, but with the same thickness,and keep the (structurally-most-practical) rectangular cross-section. They're essentially BEAMS, after all... the strongest beam is the shortest one, all other matters being equal. Put it in at an angle and you've got a longer... read WEAKER... beam! Make it wider in cross-section (ie, along the length of the vessel) and you dramatically increase the structure's strength with even a small increase.
As for the primary-to-secondary "dorsal" interconnect... this is really a pretty bad design, honestly... if I were redoing that from scratch, I'd have TWO "dorsals"... going from the centerline of the secondary hull upwards, at angles, to intersect the saucer in two locations. That would result in any bending moments between the primary and secondary hulls resulting in only tension or compression in the dorsals, not in torsion at a narrow joint! (I also think that this would have given a design which would be every bit as reminiscent of "tall ship" sailing vessels, and would have had a nice parallel between the dorsals and the engine nacelle pylons.)
That said... the design is the design. It is what it is, and it's so widely recognized, worldwide, that any change to the design will inevitably result in people not seeing it as the same ship. It might be a BETTER design, or it might be a worse design, but it's not the SAME design.
See, nobody's claiming that the original design is perfect. We DO claim that it "looks great" (and that's a matter of taste... so nobody can say "you're wrong"... only "I disagree"). And nobody is claiming that other designs can't be made... only that you can't replace one design with another and expect people to accept it as the same thing. And nobody is saying that the design as it was originally presented on 1960s TV screens was perfect... some of the "superdetailed revisions" we've seen over the past few years have illustrated that nicely... same ship, same design, but much improved presentations.
The one thing that I still don't accept is that the design has 1960's specific design elements. (You can argue that the interior sets do... that's a different conversation, though.)
Simple shapes, to me, does not "date" the thing to the 1960s... quite the opposite, in fact. "Curvy, fin-ridden" shapes with blocks of contrasting colors say "1960s" to me.
When I see the big, broad "graphics arts" panels on the 1701-E design... you know what it makes me think of? The big inset wood panels we used to see on the sides of station wagons! VERY 1960s! The simple shapes and coloration of the 1701 makes me think "modern" far more than that does.