I think this has been covered once before, quite some time ago. If I remember correctly, design asthetics aside, the in-universe explanation on why warp drive looks the way it does was that (1) the warp nacelles were kept a distance from inhabited sections of the ship for safety from some kind of radiation from the warp coils when they were engaged, and (2) since the warp nacelles had to be away from inhabited areas anyway, the engineers tinkered with hull and warp field geometry until they ended up with a workable design, ranging from the Phoenix and on to the Daedalus and Constitution-class ships in TOS.
There was even some speculation that the concave portion of the aft secondary hull that is a design evolution in most Federation ships has something to do with improving warp field geometry as well. Look at the Daedalus, then the Constitution, then the Excelsior. If anyone on here would care to discuss that, give your thoughts.
If those above items are indeed the case, that would explain why most Fed starships have the warp nacelles sticking out thusly; a trade-off in speed versus space. Tighter-in nacelles equal a smaller defensive shield bubble and less power costs to provide greater protection, but further-out nacelles give greater warp speed with less power. If it requires greater power to go Warp 8 in a Defiant-class than it does a Galaxy-class because the warp coils are closer to the body of the ship, then the Defiant has that power in spades and the ship bulls its way through space rather than gliding through it with more grace and less effort than the Galaxy-class.
Or, equally possible, whatever radiation containment restraints older designs used to protect inhabited ship sections from the warp drive have been improved over the years to the point where the warp nacelles can be embedded into the ship, a la the Defiant, Saber, and Steamrunner-classes. That could even be an outgrowth of new warp drive design that is less stressful on subspace as a result of that situation in TNG where warp drive began to wear away at subspace. But then again, we don't know the top speeds of the Saber and Steamrunner; they might be content to go along at Warp 7 or 8 while ships with nacelles further outboard can go Warp 9+.
The above explanations are as good as any I've seen thus far for "scientific" reasons rather than design asthetics.