Daniel Davies (of "shorter" fame):
My canny theory about what happened is that the Israelis had convinced themselves that the flotilla were gun-running, didn't bother to check, and acted accordingly, planning roughly the clustereff that actually happened, presuming that the justificatory material would be found after the event. And then it wasn't and oooerr, oh shit. This would also explain why the post facto media strategy (via Henry) was so totally incoherent - it was built around a corpus delicti that didn't arrive.
My take is slightly different. I think the IDF went in thinking that the ships were full of silly peace types who would be frozen in terror at the arrival of the mighty Israel military. This would explain why they went in without throwing concussion grenades first and rappelled down singly rather than in pairs. They expected no resistance. Instead, furious opposition in the form of wooden clubs arrived - a pretty gutsy thing, in fact, given they were up against guys with guns - and when the Israelis started losing the fight, they resorted to those guns. Now all they can scratch up is video of their elite commandos getting beaten up by silly peaceniks and a pile of weapons including the wooden clubs, as well as tools from the engine room and cutlery from the galley. There was even a dangerous-looking phillips head screwdriver.
So, in short, the IDF fucked up by not planning for the contingency they found themselves in, period. And a bunch of people are dead as a result.