Looking at the pic that comes up for the C-Store advertisement makes me want the Mini Nacelles to be on the MVAM Alpha section.
Someone mentioned canon for why they are gone, but in this case appearance should trump canon.

It looks more interesting that way.
Comments
They were on the alpha section while it was in beta, at least for awhile. Seems odd they removed them, unless the ship guy (forgot his name,) didn't have time to add the customizations to them.
I agree, and one of the issues I have with this being at all practical....same as saucer separation is it just can't produce the power needed for it's shields and weapons .
I apologize for any inconvenience this may cause.
Sure it can. The saucer section (which contains its own warp core) is actually bigger than the Defiant, which packs enough punch to destroy Jem'hadar attack ships in a couple hits (while the galaxy-class Odyssey couldn't touch them).
when fixed will they extend durring mva mode?
If you watch Message in a Bottle, the way the Prometheus is shown in both battles has inconsistencies.
Besides the nacelles being extended in one scene, and not the other, the impulse glow is white in one scene, and red in the other, and I think there is at least one other thing that I can't recall off the top of my head.
I do hope Cryptic continues to look at the various issues that the ship has, though thankfully most are just art issues, like how it moves visual effects from borg/aegis/reman deflector.
The only technical issues I have encountered is the pet sections tend to lag too far behind limiting how much they add to the battle, that the ship comes to a complete stop to separate (which I understand is a Cryptic engine limitation, and reasonably mild) and how the Alpha section flies, which seems strange because it has non-visible components needed for it to line up with the other sections, which is a bit disorienting. Overall I think its a pretty great ship though.
Very cool. I bought my MVAM today and I'm really enjoying it, it's nice that it's still being tweaked.
Is it also a possibility that the "pet" sections of the ship will maintain the special appearance of your ship in circumstances such as Reman shields equipped or Borg set items, as well as your customization options such as nacelle/body choices? It's kind of odd that my ship splits up and looks totally different, then swaps back.
A minor gripe for sure, but the eye candy in STO is so good that I'd be thrilled to see it preserved in cases like this.
I disagree that there is inconsistances. There was only 1 CGI model used.
As I said before, during the first seperation scene, you saw the Nacelles deploy since the ship was at Warp. But the second seperation at the hands of the Doctor, the ship was at Impulse, so there was no need for the Warp Nacelles to deploy.
As for the Impulse Engines color, there is two logical explainations.
1) During Seperation, the Impulse Engines is throttled down due to the change of mass (if you know flames, blue burns hotter than red).
2) The 3 sections share the same area for the impulse engines are shared in the same location. Each giving 1/3rd the total output. (If you look at the model, the Beta section's saucer area has an area that could be the Impulse Housing, and the Gamma there is a trailing edge that could be baffled Impulse Engines similar to that of the Nebula.
So I like to believe there is no inconsistancies.
I doubt they would enable separation at "Warp" speeds in sector space.
This is just a little nice looking gribbly that they did some Awesome work on and I want to be able to appreciate it.
Thank You I look forward to the fix!
And with the work they put in on them it would have been a shame not to use them.
The coolness should not be limited by the game engine that does not let us separate at "Warp" in sector space.
The Devs did a lot of good work on these pieces and they should be showcased.
In all of the shows there was always some confusion about, "we can still maneuver using "warp."
-Aesthetic effects from Aegis Shields/Impulse Engines/Deflectors, Borg Shields/Engines/Deflectors/Consoles, and Reman Shields need to keep their positions and be shown on all three sections when seperated. At the very least, the shield effects from aegis/borg/reman shields should remain on all three sections when deployed.
-The mini nacelles on the top and bottom of the saucer section need to appear after seperation.
-Impulse speed of the two uncontrolled sections needs to be greater than that of the player's ship so they can 'keep up', right now they lag behind
-It'd be nice if the three sections flew in formation when not in combat, right now they just fly back and forth trying to keep up with the controlled section.
-The re-joining animation always shows the stock prometheus, instead of the custom ship appearance used by the player.
Another thing I'd like to see, but probably wont happen, would be having the uncontrolled sections match the weapon type the player is using. Right now, no matter what weapons you have equipped on your ship, the two uncontrolled sections use phasers - I'd like to have all three sections using, say, plasma weapons, rather than being mismatched.
Speaking of that, it's sort of silly to be approaching a way point and seeing enemy ships all jostling around, not moving in any sort of formation, just sort of erratically orbiting a set of coordinates.
Ships aren't animals. Our separated sections shouldn't be restlessly prowling around us without any apparent reason and enemy ships shouldn't be pawing around their patrol waypoints like a caged tiger. If the captain(s) are nervous or agitated, perhaps they can stalk around their bridge or pace a groove in their ready room, that behaviour shouldn't really be reflected in the actions of their ships. (At least in "The Vault" the enemies seemed to have a set patrol pattern instead of all milling about a way point.)
I think we need to see more things moving in formation, our combat pets and the NPC (enemy and friendly) ships we encounter.
CapLogan said on the Tribble forum that there are some fixes to the Prometheus that didn't make it into this build, but would be in the next.
Yeah, that bothered me too. I been using Plasma Beams on my Prometheus for a couple of months and having the pieces use Phasers and Photons is annoying. Perhaps we will see a fix someday.