What made this plane so unique?
It wasn't unique. In fact, almost every Boeing aircraft and some Airbus aircraft use a similar fuel system configuration. Every fuel tank is like a bomb sitting inside the aircraft. Heated, pressurized fuel is very explosive. But it only explodes if it is exposed to a source of ignition. The design philosophy of Boeing is to eliminate the threat of explosion by eliminating all sources of ignition inside the fuel tank. This has proven a relatively safe design philosophy as evidenced by the incredibly small numbers of fuel tank explosions. But there isn't a human engineered system ever created that isn't without flaw. Since the Wright Brothers, aircraft have crashed because in the life of an aircraft, things happen that engineers can't predict. And sometimes, they never figure out what happened. Especially when the aircraft involved is almost completely destroyed and soaked in sea water for several weeks.
"So why didn't Boeing ground all 747s and any other planes with a tank like this?"
That would be the decision of the NTSB, and they generally don't ground fleets of aircraft (its happened only once in the last 30 years). Usually, they just order inspections on all aircraft of the type being investigated. This was done several times during the course of the TWA 800 investigation.