Stupidly high for most companies
Indies Crash E3 was an effort by developers Semiformal Studios to get itself plus ten other indies companies entry to E3 2013. After the successful voting period, Semiformal found themselves with a 600 square foot space on the E3 show floor, and with other costs and fees, spent only $100,000 on the entire show. That sounds like a lot, but here's the shocker: That's actually really cheap.
"If we hadn't second-guessed everything, worked really hard, and gotten clever it would have been about $300,000 - $500,000, but the necessity to put on a good show and the lack of funds forced us to think cleverly and work hard to make it happen on the cheap," Semiformal Studios told Joystiq. "I'm confident we had the cheapest price per square foot (when you factor in all costs) of all the decently interactive booths at E3."
The 600 square foot space cost $30,000, another $30,000 to build a booth, and the remaining $40,000 went towards E3 fees and other needs. As for the booth itself, the team was originally quoted between $80,000 to $250,000 from booth designers and museum exhibit companies before they went with a local prop-maker instead.
"Some companies literally told us that the reason for the cost was simply, 'If you want an E3 booth, you have to pay E3 prices.' Even some of the non-E3 expo makers, like the museum designers, gave that as their reason."
So yeah, there's your reason for so little indie love at E3. There are other alternatives, but ones that are typically away from the show floor itself and ultimately wouldn't be worth cost.
Breaking down the cost of an E3 booth [Joystiq]