Yeh, GPS doesn't work, big deal. I doubt many people buy tablets to use as a sat nav anyway.
The Ipad has better apps and a better eco system overall but other than that the transformer prime isn't "embarrasingly far behind" or "not even close". In fact, it has gotten glowing reviews all across the web. Excellent screen, battery life, performance and ICS, not to mention the keyboard attachment. I'd say it's the first tablet that you can legitimately say is a worthy competitor to the iPad.
You are talking about the hardware directly though. The positive reviews simply praised it as the best Android tablet, it isn't really even compared to the iPad because at the moment there is no comparison to be made.
Joshua Topolsky (editor of The Verge) has done nothing but praise Android phones, but just recently he posted this on Twitter -
After using the Prime for a week, it's clear Android tablets are still awful. Excited about new iPad, and I think MSFT has a huge opp here.
Going back to the iPad after the Prime feels like going from drowning to fresh air. Insane difference.
Like I said, it's the overall difference. Sure, the hardware differences aren't big and the Prime is better, but the software is so, so important on tablets.