If I could command any ship I would pick a Galaxy Class, and install the following upgrades:
Ejectable Warp Core
Phasers that can destroy little kamikaze ships
Phasers on the Stardrive section
The Galaxy does have an ejectable War Core, The 1701D's just didn't seem to work.
Her phasers can hit multiple small objects like in Conundrum
The Stardrive has phasers: A strip on the battle bridge head part of the ship, a strip on the ventral side just behind the deflector dish, small ones on either side of the aft torpedo launchers, and on the warp nacelle pylons.
My favorite ships:
Sovereign - looks like it's always moving and just looks good.
Intrepid - Scrappy, fast and agile and it can land.
Akira - I like the catamaran design.
NX Class - I just like that catamaran look.
Sh'Ran - giant ring looks cool.
D'Deridex - Mean and green, the double hull design is prett cool.
Breen ships are just cool do to their asymmetrical design.
Negh'var - the Klingons really made a piece of beauty and firepower.