1. Extreme temperature fluctuations. You're essentially living inside a solar collector. In the fall, the sun would blaze in through the windows, and I know you're supposed to have overhangs, shades and air vents and underground air circulation systems, all of which we used. The bottom line is you can't cheat physics. Even with the shades closed, the house is receiving over 300k BTU/hr of solar heat. This is just too much for any reasonably sized cooling system to handle. My infrared thermometer measured surface temperatures in excess of 140 deg. F on surfaces near the windows. In the winter, the same windows would leak heat like a sieve. Here in Montana when it's overcast, 10 deg. F, and the wind is blowing 30 mph the front of the house would barely reach 55 deg F. This was with the 30k BTU propane furnace going 100% duty cycle. I would work at my computer with long pants, a sweater, a blanket over my legs, and an electric heater blowing under the blanket :) The rear of the house is built into the hillside, so it would be warmer in the back, but you could never get the place past about about 65-68 in the winter no matter how much you tried. The sheer size of the front windows and lack of insulation again made the house design at odds with thermodynamics in my opinion.
For the sake of comparison, our place in the hangar has ~R30 walls to the hangar, and again about ~R25 walls to the outside. We have in-floor radiant heat provided by our geothermal heat pump. Earlier this month when it was -20 deg. F outside we were toasty warm at 74 (we have a newborn child in the house now). And we were using significantly less energy to heat than at the Earthship.
2. Mice. The house construction methods are inherently porous, and mice have infiltrated the entire structure. They live in the cavities the walls form (and the roof supports), along the utility raceways in the ceiling, under cabinets, everywhere. I surmise that the mice have tunneled through the back of the hillside, between the tires, and up into the hollow cavities which support the ceiling. They then use this space to move around the inside of the house structure to other areas. No amount of trapping poisoning, etc. has slowed the onslaught of mice into the house. If the only way to prevent mice from infiltrating your supposedly green house is to use concrete in its construction and set outdoor poison traps which potentially kill hundreds of mice and may harm animals which then consume the poisoned mice, is this really such a green alternative?
I've visited an Earthship being constructed in Big Sky Montana by Mike Reynolds this year. The design changes I've seen may partially address point 1, but as far as point 2 I'm not at all convinced that this new house will be any better. I admire his vision, and that he's been able to take his ideas so far. From an engineering standpoint, even taking into account the ecological footprint of the structure, I'm not convinced that his approach is the best when you look at the whole picture.