Mostly the fact that the thermal exhaust port didn't matter when there were even larger channels leading to the main reactor due to an unfinished structure. While the Emperor didn't plan on the Rebels succeeding, he certainly granted them access to information and vehicles that allowed them to succeed in the end.
I see, but I think you're missing the point of the scenario; the second Death Star was deliberately revealed to the Rebels in it's unfinished and apparently non-operational state so that the Rebels would believe they would be able to destroy it (and perhaps the Emperor too) and commit their entire fleet to the attack - when in actual fact it was operational and the shield generator heavily defended and expecting the commandos. It was bait to lure the Rebellion into a position where they would be broken in a single engagement; had they finished constructing the Death Star II, the Rebel fleet wouldn't have come near it as they had no way of destroying it in a frontal attack, and the Galactic Civil War could have dragged on indefinitely.
It's not a design flaw that something is not invulnerable when it's only half built - that would be like saying that all Federation starships have the 'design flaw' that they're not capable of fighting efficiently when they're still only half built in space docks. Likewise, there was no incompetence involved in Palpatine's plan, and indeed it all but succeeds - the Rebels were not able to penetrate the Death Star's shield (indeed, Admiral Ackbar was about to order the fleet to flee had it not been for Lando persuading him otherwise) and the team that were going to destroy the shield generator were all captured, and it was only a string of extremely improbable coincidences (as well as Vader being redeemed and some good old-fashioned Imperial arrogance) that caused the plan to fail.
Quote (marshall8472 @ Feb. 11 2010, 2:13 am)
in case no one mentioned it, we see parts exploding when the millenium falcon and the death star got hit by weapons too.
It's not that things explode when a ship is damaged that is the problem, it's the fact that the rear of a Star Trek ship can be hit and inexplicably cause a console at the other end of the ship on the bridge to explode.
In Star Wars, things tend to generally explode in the area of the ship that actually gets hit. I don't remember any of the Falcon's control panels exploding in Han and Chewie's faces when the Falcon gets hit; likewise, when General Grievous's flagship has a full broadside blasted into it, causing it to go out of control (and then later actually breaks in two! ), we see the damage happening to the areas actually affected, while the bridge is absolutely fine. We see explosions in the corridors and turrets of Death Star being shot, but Tarkin and the commanders are unaffected in the control room; similarly, even when a shield generator on the same structure as the bridge itself blows up, the crew of Darth Vader's Super Star Destroyer suffer a bit of tremor, but no exploding bridge consoles or other random damage.