I love the auctions because they make the game less random: there's no benefit to drawing the first position when there's an obvious pick for a faction, nor to drawing the last position when there's none and only one great booster.
It also serves to make the weaker factions more playable. I like playing all the factions (love the Lantids, but even like the occasional Gleen game), but its quite rare for it to make sense to pick Gleen over the Taklons or Ivits when there's no bidding.
I also don't really like picking a faction first when there are three more players to pick and you've essentially got no idea what game you'll end up playing (I know it is still technically a perfect information game, but it clashes with the 0 randomness aspect that I love about Gaia).