Interesting thread, Tails! I'll try to answer this as honestly as objectively as possible.
ONE Mane Six character: With the first overall pick in the Equestrian Friendship League, Alfonzo Dennard selects... Twilight Sparkle, Magician, Princess Celestia's School for Gifted Unicorns. Let's face it -- this is probably an unanimous selection. What's there to be doubted here? If there's any pony in Equestria to save it from danger (and she has proved it on more than one occasion), it would be her. She's got the smarts, wit, charm, drive, passion, and faith to bring it from the ground up and that includes rescuing it from the various evils that come into contact with the magical land on occasion.
Need to draw up a new strategy to get through an obstacle? No problem, that's her forte! How about creating spells to your convenience? Absolutely; she's already a master of magic! And how about a shoulder to lean on whenever you're in doubt, feeling sad, or need cheering up? Just talk to her and she'll tell you that everything's going to be all right, spoken in such conviction that it'd be enough to rattle the cages of even the most cynical-hearted of folks.
ONE side character or minor villain: Trixie. She's a master of illusion magic, and by my estimates I figure we could eventually devise escape plans in case we run into a scenario where we're overmatched somehow, either by bigger, stronger guys or just outnumbered. It's sometimes smarter to run than to fight -- while I would gladly beat the ever-living hell out of any threat that could harm Equestria, there's no shame in retreating and regrouping. Plus I love the attitude she displays -- lots of heart and passionate about herself, though it's not so much boastful anymore! Very endearing in its own way.
ONE of the Cutie Mark Crusaders: Apple Bloom. Contrary to popular belief, a filly can demonstrate greatness in her special ability even before she's discovered it. In Apple Bloom's case, she clearly appears to be adept at carpentry and design; this would be a huge convenience for anyone because saving the world usually means you're constantly on the move with your pals. In AB's case (and to quote Obadiah Stane from Iron Man), she can build something from a box of scraps... perhaps from inside of a cave. This means we'd get quickly-built housing serving as a temporary residence until we're ready to move out again, just to rest and recharge our batteries. With all of the other homes being potentially being burned to the ground due to attacks, I'd say acquiring shelter is a very underrated aspect of going on a lengthy mission such as this one.
ONE stallion: Shining Armour. Because you just can't turn down the chance of drafting not only a high ranking officer of Celestia's elite forces, but the commanding officer himself! His training is exactly what's needed for this sort of mission -- Shining, like Twilight, has the intellect and aptitude to get it done. Although he's definitely not as smart as his sister, he's got the big advantage in size, experience, and most importantly - physicals. I have no doubt that being able to exert yourself quite a bit will be critical at some point in the mission -- like moving huge boulders out of the way or getting something done by brute force alone. Close-quarters combat is another thing that could pop up -- who do you give the edge to? Shining.
ONE background pony: Flitter. I'll take the speed and the ability to fly (to possibly scout for certain things) here, plus she just looks like a total sweetheart. It is important to gain the positioning advantage over an enemy force that just so happens to have invaded your homeland, and this could change the game around.
ONE non-pony character: Spike. He gets lost in the conversation more times than I can appreciate -- everyone's so worried about ponies they forget about the little dragon that's often been a big part of their plans. Other than being a communication medium in contact with Celestia, it's important to note that he has good size. He's nimble, quick, and for his age and size, he's bright and strong, respectively. That makes him a good candidate to send out on recon once in a while either to scout on foot while at the same time being out of sight, because of the fact that he'd be hard to see due to his small stature. This also includes letting him go into some small spaces to get things that would normally be out of reach for larger folks because they're so big. Also... free fires! This often gets lost as well, but creating a source of heat and light on the go is important if you want to stay fresh throughout the journey.