Bingo. The T-X is superior to the T-1000 in every way.
The T-1000 series was deemed an "unstable" unit by Skynet - since it's got no centralized CPU, it's very easy for the unit to "go rogue", and that poses a serious problem for Skynet, since T-1000s are expensive to produce, and even MORE "expensive" to disable if they stop obeying orders.
Beyond that, the T-1000 is made up of billions of nanoparticles, and it's not exactly difficult to render those "inert". If you dealt the T-1000 enough damage, you would manage to disable enough of it that it would no longer be a threat. The T-X doesn't have this problem - the T3 novelization even goes as far as to point out that you can't melt down a T-X, nor can you crush it (and before you point out the T-X losing its legs at the end of T3, the T-X intentionally disconnected its own legs, because it'd have taken too much time to free itself from the chopper otherwise).
Also, there's multiple scenes in T3 which point out that a T-1000 would not have been able to complete its mission, while a T-X nearly did:
- the T-X takes an anti-tank rocket to the chest, and it merely damages its plasma weapon. The T-1000 took an M79 grenade to the stomach in T2, and went down screaming.
- How, exactly, would a T-1000 get past the magnetic field generator? The same magfield generator that was stripping away the "liquid metal" exterior of the T-X.
- the T-X is hit by a helicopter, and totally loses its liquid-metal exterior. That implies that if a T-1000 took the same hit, it'd have been all over the walls. Given that, it'd have taken too long for it to reform (assuming it COULD reform) and John Connor would have escaped under the blast door with ease.