The stock twins are kinda small, and the huge cast-iron manifold they connect to is a huge heat sink, keeping tons of heat in the engine bay. Additionally, the sequential nature of the turbos means that it is vacuum operated, and once one line goes bad, it can screw with the entire setup.
It's best to upgrade and go with a medium turbo, either a T04R, or a GT35 series turbo. For crazy horsepower, one can go up to a huge T88, or GT40 large frame turbo. Smaller aftermarket twins work well in MKIV's, but generally don't have the top end of the big-ass turbos.
The only factory turbo setup that seems to be working really well is the setup on the RB26 motors. They're not sequential - rather 3 cylinders per turbo. The manifolds can accept any small-fram Garret turbo, and the engine responds well to either a pair of bigger T28's, or with a new manifold - a pair of GT285's. Again, some tuners have used two T3/4's, or two GT3037's - but you can't mess with a T51, T88, or GT40.