Okay, what I like: The stairway in the middle of the control consoles is an excellent homage, the "energizer" (or whatever they are) structures you have down there are brilliant, it all really does JJ-Trek the enginering room nicely.
Things I'd like to see change: If this where a ground based facility, then an open pool of coolant fluid probably wouldn't be a big deal, but as much as a starship gets knocked around, I expect it'd be pretty problematic. Also, I'm not sure I get the fan either...
What I'd like to see: Besides the console along the wall with the stairs running up it, the two features which really make the (season 2 and 3) engine room set for me are the dilithium pedestal thingy and the so-called "cathedral pipes" behind the mesh. I'd love to see your take on these two elements. Maybe flooring over the water and having a big burly, somewhat trapezoidal piece of machinery in there and doing something behind a grill in the wall that looks like the biggest damn V-8 we ever saw!
Wonderful start though.