I feel the aft needs some serious reconsideration; it's not the fault of the nacelles that they don't look right, but those curved pylons are part of the problem, too. Though of all three designs, I like the straight-nacelled version the best.
By the way, what program are you using?
The aft is problematic, yes; I'm still fiddling with it. I can simply straighten it out toward the end; but that would be too easy. I think it makes the whole thing stand out so I'm a bit inclined to at least keep that part. But I agree, curved nacelles is perhaps too un-Federation like; I've gone for the straight ones.
I use
modo.
The curved catamarans don't seem to serve a purpose. Maybe attach the nacelles to the end of them instead of using pylons at the mid length? Also, the entire ship needs more of a vertical element. It's too flat. Maybe have the catamarans curve down as well as out?
Well, being aesthetically pleasing is a purpose in and of itself, as well.
You're right in that it needs a vertical element. After much trial and error, I've decided to put the nacelles down, add a much more prominent secondary hull and made the whole thing higher in the Y-axis. Does it look better?
I'd rather have the impulse engines on the tips of the catamarans (straightened out NX-Class style) & the #3 "straight" nacelles mounted on the dorsal side of the catamarans at a slight thirty degree angle. Dual navigation deflectors (see "U.S.S. Phobos / Loknar-Class TMP Refit".)
I don't like dual navigation deflectors; one is quite enough I think. It also makes the engineering hull look as if the ship's 9 months pregnant. Of twins.
Perhaps a tiny deflector in the saucer. The idea about the impulse engines on the end of the catamarans is a good one, after all, with them coming out of the saucer and the shuttlebay where it is, there's hardly any room to put them in the traditional area. As a matter of fact, that's what I did.
I was thinking with the pylons... curve them out as they are, but straightern them out 1/2 way through...
...as for purpose, easy to figure out once it's done
I can simply make them straight, but that will make the rest look much more traditional. I'll do it as a last resort, but first I'm still trying to make it work.
And yes, purpose can be figured out afterward.
I am leaning toward some sort of Akira successor or relative (obviously), probably after the TNG era. Perhaps in the Movie universe, who knows. Depends on if the design will fit enough or not.
Think along the lines of the "Rebel-Class" seen below.
http://www.feymanshipyards.com/CruiserRebel.html
Hmm, I don't think I'll be going in that direction. Nacelles sweeping back and up give me a more of a "soaring majestically through space" feeling. That's good for something like the Enterprise, but this ain't no enterprise. And it's not a Romulan warbird, either. I'm trying to keep it elegant instead of clunky but also rugged instead of majestic. Elegant and rugged. Difficult combination, now that I think of it. Oh well.
[...]
it looks like they need some sort of follow-though. They need to DO something... maybe the nacelles need to be more integrated with them.
Yes, it doesn't look very cohesive yet, I agree.
When they curve inward they create this weird angle, combined with the roll bar's angle, and you're left with just a ton of different angles all in one area.
Your ship looks good. Not really what I'm going for, though; it's very curvy. I agree that it still has too many angles. Some will have to be eliminated.
Here's a quick and dirty sketch of where I think you should go with your wonderful bi-hull design. I think this approach would eliminate the feeling that the pylons & nacelles are just sort of "stuck on" somehow.
It looks interesting, but also off, somehow. Probably because the curved rollbar dominates too much when there's no shape to break them up. Both the Akira and the NX class also breaks up the pylons/rollbar for that purpose. I'm actually inclined to simply fill the empty space right up to the catamarans, remove the nacelles and give it a bit more mass in the back so it'll look like a primitive Wells class.
However, I have tried to cut off the catamarans a little bit after the rollbar, but it simply looked even more odd then it does now. I'd have to straighten the ends up for that to be workable, and I'm not inclined to do that yet.
Yeah the pylons ending like that pointing outwards just looks very odd.
If you insist in leaving them like that
I would suggest attaching the warp nacelles at the end of the pylons, instead of branching off of them.
It does. And I insist.
I'd like to try and make it so that they do fit. After all, the double hulls on the Akira are very, very odd also, if you look at them separately.
And for those I couldn't think of a big reply: thank you for your comment.
I didn't expect so many replies. Good to see there's interest; at least it means the thing isn't dull. 
And if you ever get the chance to look at the 
