but seriously why do I see so few nebula class starships in the game ?
Because of the perception that it has been made completely obsolete by other ships.
Most notably the Tholian Orb Weaver.
A bit of history here:
There was (still is, technically) a thread by a guy called Cygone which proposed a method by which a Nebula could be made into a respectable Damage Dealer/support vessel hybrid.
This was prior to a bunch of patch changes, during which Tricobalt Mines were buffed, the damage from Photonic Shockwave was nerfed, and certain Tactical consoles no longer buff all forms of Kinetic damage (so you can't buff both Torps and GW3 with the same "+Kinetic damage" console). And also prior to the release of the Tholian lockbox ships.
The "Tholian Orb Weaver" is basically a Nebula with better Bridge Officer slots and an extra Tactical Console.
Essentially, if you can make a good build in a Nebula, you can make it better in an Orb Weaver.
These days the best damage output from a Science ship in PVE will usually involve either going down the [2x Torpedo Launcher/DBB Fore + Turrets Aft] route, or multiple Tricobalt Mine launchers. BOFF abilities to maximise this damage will be Attack Pattern Beta (to buff all damage types) and/or Dispersal Pattern Alpha (not Beta) for extra Tricobalts. [Torpedo Spread also deserves a notable mention, since if you are able to tightly cluster multiple foes together with Gravity Well then a Torpedo Spread from a high-base-damage launcher can cause huge amounts of overlapping splash damage].
Polarized Disruptors have been a nice addition to science vessels though. The Disruptor Proc is obvious, but the Polaron drain ties in nicely with Tykens Rift II and the inherent Beam:Target Shields.
An example STF/Fleet Action setup would be this build, which translates into this on the Nebula.
I currently run a similar setup on my Orb Weaver, and still have a (mothballed) Nebula in the shipyard.
Note the use of TBR3 instead of GW3 for damage there - Aux2Bat allows a high uptime of all BOFF powers and reduces Ship Aux to minimal levels whenever it fires. Low Aux power is essential for maximised damage from TBR3 in order to reduce the inflicted repel and allow all damage pulses to hit. Deploying GW1 upon a group of foes therefore allows you to hit everything with a variety of extremely heavy AoE damage, including TBR3, and splash damage from both Torpedo Spread and/or Tricobalt mines. (Technically you could remove Aux2Bat1 and replace it with EPTS2, then take TBR1, Tyken's Rift 2 and GW3 in order to trade a little damage for more versatility... I have those powers on my other Sci BOFF and a spare Engineer to allow me to run both as-needed)