I used to have the Death Star 1 and 2 tech manuals for the old SW RPG. It described that the DS2 didn't have the ventilation port weakness that was exploited by the Rebs in ANH. Rather than large vent ports like on the DS1, they were much smaller and more numerous. However the DS2 was still in the construction phase, so it had entire huge sections exposed.
I must agree with others that when Palpatine said that the station was operational, what he meant was that the superlaser was operational. As for turbolasers and self generated shielding, it's a moot point. The shield generator on Endor was still emitting the shield, and the superlaser could fire through it. For all purposes the Death Star 2 was completely protected. Add in the full might of the Imperial armada (extreme overkill) and by all sane means it ought to have been a flawless victory for the Empire.
The biggest weakness on the DS2 operation was the Emperor's overconfidence (just as Luke says). Emperor P didn't count on the Ewoks being able to reinforce the small rebel task force on the moon. Because of the Ewoks, the rebels were able to lower the shield. Add in Anakin Skywalker (Darth Vader crossing to the LS) killing the Emperor. According to EU sources, the Emperor had been performing battle meditation to coordinate the Imperial fleet and give them courage. According to Grand Admiral Thrawn, the Imperial fleet went into complete disarray after the Emperor was killed. If you think about it even with the DS2 destroyed, the Empire still should have been able to win. Just compare the two fleets. (We get a good idea of how big the rebel fleet is just before and after they make the jump to hyperspace. The Imperials fleet is visible right after the DS2 fires the first time. It's WAY bigger than the Rebel fleet).
Because the Imperials were without the battle meditation for the first time, they lost the will to fight.
Even with whatever secondary defenses the DS2 might have had operational, none of them would be able to withstand a collision with a super star destroyer (a.k.a. the Executor).
No I definitely would not say that the DS2 was useless. I think it was just super unlucky.