Believe what you want, but as someone who has had inside knowledge of the festival's bookings for the last few months (LA music industry is very small), I promise you that out of all of the headliners, Phoenix is the one that has been expected to be headliner for months now.
Phoenix headlined Lollapalooza in 2010, so them headlining Coachella in 2013 right around the time of a new album (and therefore new singles hitting radio just before then and an increased presence) is not that weird. On their last major tour, in 2010, they played almost all arenas or bowls except for smaller markets, I don't know where you're getting your average 2,000 attendance number from. Hollywood Bowl? Santa Barbara Bowl? Agganis Arena? Don't pull numbers out of your ass.
I give you one thing, there was supposed to be a very strong subheadliner on their day to help in things, and that artist pulled out, but either way, Phoenix is definitely big enough to be top line on this.
Those are the dates with the venues listed that sold out.
October 27: The Fillmore, Miami Beach, FL, USA – SOLD OUT Cap: 2,500
October 26: House of Blues, Orlando, FL, USA Cap: 2,000
October 25: House of Blues, Myrtle Beach, SC, USA Cap: 2,000
October 23: Tower Theatre, Upper Darby, PA, USA Cap: 3,000
October 22: Ricoh Coliseum, Toronto, ON, Canada Cap: 7,500
October 21: CEPSUM, Montreal, QC, Canada Cap: 5,000
October 20: Madison Square Garden, New York, NY, USA – SOLD OUT Cap: 20,000
October 18: Agganis Arena, Boston, MA, USA Cap: 7,000
October 17: Cornell University, Ithaca, NY, USA – SOLD OUT Cap: 5,000
September 26: PNE Forum, Vancouver, BC, CAN Cap: 4,000
September 23: The Rail, Salt Lake City, UT, USA ◊ (Please note that this date has been moved to In The Venue) Cap: 1,500
September 22: The Pearl, Las Vegas, NV, USA Cap: 2,000
September 21: Open Air Theatre, San Diego, CA, USA Cap: 1,200
September 19: Santa Barbara Bowl, Santa Barbara, CA, USA Cap: 4,000
September 18: Hollywood Bowl, Hollywood, CA, USA -SOLD OUT Cap: 18,000
85,700 seats available and to be fair, we'll say that they sold out almost every show with 80,000 seats sold. Average still goes well above what I projected at around 5,000 but that average goes way up because of the bigger shows (LA, NYC) and if those are taken out, the average is about 3,000. Still far off from what I said but I still don't think that a band that (1. has had a mass following for one record 2. won't have a new record out/will just barely have released it) should be headlining Coachella. People thought The Killers were questionable headliners and they had 3 massive records out. Also, Phoenix was main support for Lolla. Green Day was headlining but played at the same time as them.