What Science skills do you use? I've just leveled an Engineer in a Nebula and found it was very effective against the Romulan NPCs. Like all NPCs they're very susceptible to power drains and will do nothing to clear debuffs so skills like subsystem targeting, Tyken's Rift and Gravity Well are very nice and make easy work of the NPCs.
For equipment, if you find you're taking a lot of damage the first thing I'd look at is a Resilient shield; it has less capacity than the Covariant you have but it takes only 5% bleed through damage (usually 10%) which can make a mess of the weaker Science ship hulls. If you only PvE then a Resilient shield with the [Dis] modifier will help by reducing Disruptor damage by 20%.
Weapons are personal preference but I prefer beam arrays and torpedoes, usually 2xBA and a Torpedo at each end. Again it's personal preference but it works for me so I run with it.
The Deflector looks as though it's not really going to be helping you at low levels. it has no [FlwC] modifier to help your inate subsystem targeting skills, the slight stealth sight increase isn't overly useful for PvE and the Romulan NPCs don't use any power drains for the Power Insulator buff to help against. Ideally you'd use a Deflector which increases the stats related to the skills you use but I don't have those details to recommend one.
The Engine looks like it'd be OK but in a Science ship you're probably running low engine power and at lower levels you won't have access to the Engine Performance skills so you'll not benefit from the engines speed at higher power levels. I always run a Combat Impulse Engine at that level and keep the power setting at 25. My ship may be slow but my skills benefit from the higher Aux level.
Consoles I tend to run those that increase the skills I use or buff important abilities. IIRC my Console layout at Commander was as follows;
Shield Emitter console
Shield Emitter console
At the lower levels the consoles are very weak so I just ran defensive consoles with the exception of the RCS which was only there to help with getting the nose on target (for the Tyken's). You didn't mention your class but this was for an Engineer (hence the Shield consoles which buffed my RSF) but it should help Science as well.
The Nebula was a good choice though, a really fun ship to use and surprisingly tough too. I have my Engineer rapidly approaching VA now in the T5 version and the practice at lower levels really helped, it's a very effective ship.