I am a VA1 and currently flying the Long Range Science Vessel Retrofit (Intrepid) . I've been thinking about this and was wondering: would I gimp myself if I chose to fly the Advanced Research Science Vessel Retrofit (Nebula/Magellan) instead?
The ARSV is more of an engineering-related science vessel as it has a Lieutenant Commander engineering station, rather than the LRSV which is a full-on science vessel. Also, the ARSV has a Lieutenant Universal slot which allows for some variation.
I use the ARSV for my engineer and it's quite nice using the Lieutenant Universal station for an engineer bridge officer - that way I have 5 engineering abilities and 5 science abilities - lots of heals and fun! It's excellent at shield-tanking (when using the appropriate abilities) as well.
I've been using the Neb for my science officer, (I can see how power levels might make it even better for an engineer), and it took a while to get used to, but I'm enjoying it quite a bit now. Maneuverability can be an issue but one of the blue rcs consoles and the aegis engines really help a lot (borg set for the rest). I split the difference between beam-tanking with a variety of heals and using gravity well 3, warp plasma 2, evasive maneuvers to get in a little extra damage. The Reman BO also works nicely in the universal slot if you find you're taking a lot of damage. It's not really a super dps setup, but has been fairly survivable in pvp with enough heals left over to help out the team.
Nebula offers you a unique opportunity to change your BOs and adjust them to your mission ahead. Its a great ship if you want to do lots of stuff with your ship, Intrepid is great if you want to focus on science skills only.
i personally feel the nebula type requires more skill to use "effectivly" but otherwise is a ton of fun to fly, wanna be a big old slow escort? 3 cannons front, 3 turrets rear, rapid fire 1 and attack pattern beta 1. let loose the pew of war!