You are commissioning a new Starship. It's got all the latest high tech bells and whistles, and is going out on a mission to protect the Federation and Equestria!

The ship has everything it needs... except for someone to sit in the captain's chair. Or rather... Somepony.

Best Pony to captain this new ship, and why.

My inner debate is flipping between Rainbow Dash and Twilight Sparkle. Twilight may be a little neurotic, but she's got the Picard/Diplomat thing going on. Dash, on the other hand...

Discord: "You bucked me! Celesita never bucked me!"
Dash: "I'm not Celestia."

I think it matters when in Star Trek this takes place. Have the Borg been encountered yet, is the dominion war looming on the horizion? The time and political envirement encapsilated within said time helps to define the kind of captain a ship needs. Granted I'm a Picard fanboy who thinks he was a truely awsome captain and handled the spiraling events of things incredibly well considdering how things went to shit on him after Q introduced them to the Borg. Yet I'll admit that there are situations where Kirk or Janeaway might have handled things better, though I don't know if Kirk is the type you want fighting the Borg. I can't see his view on the no win sinario being well suited to dealing with a foe like the Borg. Though he'd probibly handle Q quite well.

Twilight all the way, she embodies the perfect level of cool headedness plus studious to fit the mold of the captainship

I'm torn between Luna and Twilight. Luna mainly for her knowledge of the stars, but she does have the authoritative tone and attitude that would make her an excellent choice in a combat or diplomatic situation. Twilight however, is more knowledgable in general, and her eagerness to study and learn would be perfect in exploring the final frontier, although she might panic in a fight against the Borg.

Luna, however, would just hurl a moon at them

I AM TWICUTUS. U WILL B ASSIMILATED. RESISTANCE IS FUTILE.

I always thought Applejack would make a good officer, though I don’t know if she’d be the best captain. I just can’t see the element of honesty bluffing her way out of a conflict like Kirk.

I vote for Pinkie Pie, in charge of an Intrepid-class vessel. The Borg wouldn't know what it them.

I agree with janushyde. What time period of Star Trek is this?
if OS, I vote Applejack, for her fighting abilities that would come in good use against the klingons.
if TNG, anypony of the mane 6 BUT Fluttershy. The other 5 would all be good at this time, if for different reasons.
if Voyager, Luna or Twilight. Insert VaporingRat's reasoning here.
if DS9, I vote Diamond Tiara, just cuz I'd like to get rid of the one pony I think has no use.
Number one, raise shields and brace for the impact of the proverbial flak coming our way.

Oh I think Prince Blueblood would be the perfect Captain ...of the Excelsior, Space-going version of The Great Eastern or the Titanic! (Look up the Great Eastern! Itwas such a bad-luck ship it was eventually wrecked deliberatey and sold for scrap...)
AJ or Dash for ToS Enterprise (With Science Officer Sparkle; "Fascinating." )

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Hold Luna in reserve as an Admiral. Give Twilight Sparkle the center chair on the bridge. She's the type that would eat Responsibilityuns instead of Funyuns (to paraphrase _The Onion_). And you KNOW she'd run a tight ship.

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Diamond Tiara as a starship captain? Now THERE'S a scary thought.

Captain Tiara: "Oh, look, it's a stupid little Pakled ship. They're not even formal members of the Federation, the little Blank-Flanks! Set phasers for light hull scoring, and carve the words 'KICK ME' onto their aft hull."
Commander Snips: "But captain, that might provoke an international incident."
Captain Tiara: "What are they gonna do, run home to their mommies? Fire!"

1276582 remember i specified ds9. the jem'hadar would be dying to take her out if they knew what she was like. pun intended, if you get it.