1. Imp vs Imp and Rebel vs Rebel are fine, and happen often. In the local tournament I played in last weekend I flew Rebels and played against Rebels in all my games. As to lack of factions, the game is based on the time period of the original Star Wars movies. In those movies it was the Empire (and their agents) vs the Rebellion. While people often try to give reasons for a shoehorned in 3rd faction, it always comes off as wish listing in a way to take ships from both.
2. Depends on the points involved. In tournament play you're looking at 100 point games generally. The highest base cost of a single ship released thus far is Han Solo at 46 points (the Decimator has a pilot that will match that cost). This is about the equivalent of 4 basic Tie Fighters (lowest ones cost 12 points). I would however give a slight edge to the Tie fighters in that fight. As to the rest of this one, I'd forget every jaded thought you have about
40k when you approach X-Wing. All the units have uses (even the big ships), all the units are worth picking up for more than just cool shelf ornaments (though that's how I started my collection), some may see less play than others, but there is nothing in the game that is outright a bad purchase. Keep in mind that the epic ships (so far the Rebel Transport and the Corvette) have their own format that is balanced around 300 (solo) - 400 (team) point games.
I've never played any of the missions, even during casual play. I've pretty much stuck to 100 point games. There are epic format tournament rules, so you could potentially play the Corvette in one, but it is more likely something you'll use in casual epic games with friends. Corvette has some cool crew cards for the regular game, if you get a chance to buy one on the cheap C-3PO pairs up with a Falcon nicely.
You can make a "smuggler" fleet using generic pilots, the one that comes in the Falcon set is even called Outer Rim Smuggler. If you want to say they're named something else that's up to you, but there are no rules for making your own pilots.
Shuttles are one of the best point for point ships in the Empire/The Game. For 21 points (this is same cost as the lowest cost X-Wing) you get a ship with 3 attack dice, 5 hull/5 shields, 2 crew slots, a System Upgrade slot, and a Cannon slot. That's a lot.
This article has a pretty good run down of the popular shuttle builds.
Edit - You are only limited to Tie Fighters if you choose to be. The Corvette and the Transport are the only two things released so far that aren't part of regular play.