Due respect to Messers. Probert and Roddenberry, but I have a notion that explains how three-nacelle rigs could function....and why they aren't common in Starfleet. I also explain single-nacelle ships without having to resort to the "dual inline coils" handwave. I draw my inspiration from the world of mundane electrical engineering. In order to do what it does, warp engines must involve a cycle of some sort, a sinusoidal (if not actual sine wave) somewhere at the foundation. Which implies circular geometry, like conventional electrical generators.
So, lets think about phase relationships. US standard 110 Volts Alternating Current can be represented by a circle with a "radius" of the difference in potential, 110 volts. The centerline of the circle is zero, neutral, the "top" of the circle is +110, the bottom is -110, and as the radius rotates around (as part of the cycle) the actual voltage varies at any given moment on time; but it switches back and forth 60 times per second (or 50 times, in Europe. Frequency cycles in CPU's do this billions of times per second, +/- 3v. The voltage on your electric range or dryer (220VAC) is accomplished by having two taps on the generator, 180 degrees apart; therefore when one side is at maximum (+110), the other is at nadir (-110), and the difference is 110-(-)110, or 110+110=220. But they are in exactly the same phase relationship. File that thought for a moment.
Let's take the case of a single nacelle, and assume it's just like that 110VAC line, a radius of the circle representing the power output of the warp core. The cycle goes back and forth from extreme to extreme (but designed to always push "forward" in warp, like the crankshaft of a steam engine). What does that suggest to you? A potentially rough ride, on the microscopic level at least; inertial dampeners take care of that on the human-detectible level. As such, a single-nacelle ship will do the job, but it is not going to have a long operational lifespan. Which is why, Gentle Reader, single-nacelle designs are exclusively destroyers, scouts, and (like the Kelvin) wartime-construction science vessels. Specific design reinforcements can mitigate these harmonic stresses, but never eliminate them altogether. These vessels are frankly expendable, quicker to build than two-nacelle ships, economical during a wartime economy, with simpler engineering infrastructure, and are expected to be expended. As the Kelvin was. And this is also why, while a multi-nacelle ship can go to warp with a single nacelle, it is, in the words of "Hunt for Red October", possible....but not recommended. Captains of damaged multi-nacelle vessels don't want to worsen their vessel's condition, if they can avoid it!
Two nacelles, in single phase, but 180 separated in the warp cycle will therefore have twice as much "pull" (that is, top speed for the ship), but also share some of the characteristics of that single-nacelle ship. Haven't you ever wondered why, in the free-ranging TOS era, Constitution-class and similar vessels had to return to base every five years or so for extensive refitting? AND why they make such an awful racket when the engines wind up? Harmonic stresses!
That's TOS. Something different is clearly going on once we hit the "flat nacelle" movie-era refits, because going to warp has problems we've never seen before -- the wormholing Enterprise did on its first attempt to go to warp. Fiiiiiirrrrrrreeeee Phhhhooooottooooon....
I would venture to guess that instead of going opposite, the nacelles are being kept in tight synchronous lock, in the same part of the cycle at all times, an engineering feat not possible during the TOS period. You still get twice the "pull" of a single nacelle, and the Federation does seem to favor speed, but with new engineering, the stresses are mitigatable....as long as you have two nacelles in balance,
OK, now to three-nacelle ships. I dislike the use of the term "dreadnought" for all three-nacelle ships. The Federation-class was a true dreadnought, larger and heavier than a cruiser, with, the designation implies, some limitations on its mobility. But other designs, like the Franz Joseph Ascension-class, are based on other hulls, such as the Decatur/Belknap light cruisers. And being a fan of that era, I regard them as canonical, period. Roddenberry signed off on those designs, back in the 70's! He had to! Anyway, the nomenclature I've arrived at is to refer to any 3-nacelle vessel as a "trireme", a nice historical term. So, all dreadnoughts are triremes, but not all triremes are dreadnoughts!
Three nacelles do work, but the have to be balanced differently, with a 120-degree phase offset. Websearch up a graph of three-phase electrical power. It would be challenging, but not impossible. What does three-phase warp drive do? It gets you about 94% of the output of the conventional 2-nacelle setup (208VAC vs. 220VAC, to use my previous analogy), and it provides more even and consistent application of power throughout the energy input cycle. Absent the stress fluctuations, trireme/dreadnought hulls don't need the ability to "flex" as much, meaning they can be built with the Treknological equivalent of regular steel instead of spring steel. Heavier, more rigid...can you say "armored"?
The downside of course, is the extra material that has to go into building each ship. Also, a trireme has another engineering challenge; they have to have hot-swappable intermix-balance profiles for both three-phase and single-phase mode, for all three nacelles and for each possible combination of two nacelles, and for each single nacelle (especially the saucer-section nacelle, in case of separation). It's easy to see how Starfleet's Logistics Division would throw up their hands and say "it's not worth building these suckers"! This is an institutional bias that remains largely in effect.
So, then, why return to that experiment, with the Niagra-class glimpsed in the wreckage of Wolf 359?
Ecological friendliness.
Remember that bit, late in TNG, where warp drive was found to be damaging to subspace? Voyager's variable nacelle pitch was ostensibly a solution for that IIRC, but what if that wasn't the only solution? Remember how I said that three-phase "pull" is more even? Therefore, it seems to me, it would be less "ragged" and less damaging to subspace. But of course, someone in the Starfleet Corp of Engineers eventually found yet another solution that didn't involve wonky moving pylons or those despised third nacelles, aka the Enterprise-E nacelle design, so Starfleet (in keeping with its institutional bias) went with THAT instead.
But there really could be three-nacelle ships if you wanted. I can make sense of four nacelles, too (that's for another post), but I'll say that five or more gets into a realm of "diminishing returns" somehow.
How's this for a debut post?