If I designed the Enterprise, I would include more physical weapons beyond the photon torpedoes (with energy yield only). I would include a rail gun and a large bore cannon, as well as missiles. Mixing ordinance preserves options of graduation of scale with weaker ships. I would also fire missiles with anti-matter warheads.
The advantage of energy weapons is that they do not have to be restocked at a resupply point, They already have a pressor (Deflector) beam. Combine that with a tractor beam, and you can shear ships into pieces....
The transporter is an interesting device. We have a quantum entanglement transporter working on single atoms. It may be used to refill fuel tanks in flight. This would allow smaller fuel tanks which are easier to accelerate initially, refueled in flight would still allow deceleration at the end of flight.
The trek transporter supposedly converts matter to energy, then reassembles that energy back to matter. If it worked, I would send a ship with minimal crew quarters, and beam needed crew members into the ship upon arrival. A dozen or so stored crew options would allow you to crew a full starship. You could beam multiple identical crew members as needed, with no logistic loading in transit. The stored crew, could travel in multiple ships. They do the same thing for objects with their replicators....
This would place the crew inside a computer, in storage, interestingly enough.
RE: I spent the evening with my Son...and Captain Kirk, fun visit for all!