From a quick look, I'd do the following to the Nebula:
1.) Ditch the scan, or fix it. And I mean fix it as in adds a bonus to sensor scan and target subsystems. Heck, you can even do it as a group-wide bonus to be activated. It would almost guarantee to push the Nebula back into mainline combat groups. Giving a science ship a bonus to sense stealth (which doesn't work, so I'm told), is completely worthless right now. The console, like many others, should be brought up to par to make people want to buy these ships.
2.) Ditch the 4th engineering slot. I don't care what niche they think the Nebula can fill with it, but they're completely disregarding the Nebula according to cannon (although, they seem to love to do this with cannon ships, aka Galaxy): if coding for a mission pod is too great (that's a "duh" moment, tbh, if they can't setup an exchange properly), then console/Boff setups are going to be how you signify this important aspect of the ship. It's a highly-modular craft, so give it a 3/3/4 at fleet tier. This lets you do all sorts of fun builds, regardless of turn rate.
3.) Give it more costume options. The Galaxy has 3 base, 1 CStore, and 1 at the higher tier. The Nebula, which was made to be a cheaper workhorse from said parts, should have more than just two costumes. I'd love to have the Venture parts, but I'd settle for just a couple more mission pods. There are at least two others they could toss in, one of which is actually cannon. While honestly I'll still stick to the traditional Nebula look, I bet people would buy the pack if they could customize the ship a bit more.
4.) Give her more hull. For Christ's sake, the Armitage has more hull, and it's still supposed to be an escort! Look Cryptic, if you want the Nebula to be a cruiser/sci hybrid with lower turn rate and more equal engi/sci consoles, then make sure an escort can't have more hull than a freakin' cruiser, okay? This is why your game is broken, because you can't figure out what you want to do with science in general. But the borked science skills are another rant for another day.
So in general, they need to un-nerf the console, balance the console slots, more hull for its reduced turn rate, and more costume options. Do that, and I bet more people would buy the Nebula as well as the Intrepid.