I am at the end game of a long campaign, and I went to upgrade a custom ship I had made.  As I looked though, I started to realize that the latest upgrade isn't the best.  

Example:

Singularity Driver: 16.2 Kinetic, 5 Thulium, 5 mass, 12 manufacturing cost

Quantum Driver:  13 Kinetic, 3 Thulium, 5 Mass, 12 manufacturing cost

Graviton Vulcan Gun:  11 Kinetic, 1 Thulium, 3 Mass, 8 manufacturing cost.

Breaking it down by manufacturing efficiency: 

S - 1.35 Damage per cost

Q - 1.08 Damage per cost

G - 1.375 Damage per cost.  Graviton is most efficient at manufacturing cost

Thulium is almost self explanatory with G having 11 for 1.

Break down by space usage (most important)

S: 3.24 dmg per mass

Q: 2.6 dmg per mass

G: 3.66 dmg per mass.  Again, most efficient by far.

Edited to add:  In the research order, Singularity Driver should be top dog (last upgrade), Quantum Pulse in 2nd and Graviton in 3rd.