Don't be scared by the 2.5L in the GS. I've driven the both the new GS250 and GS350 around the track and they are both great cars.
The tuning on the GS250 makes the engine more responsive than the IS250 setup.
The GS will also be loaded with up-to-date features, whereas the IS will have to make do until the new generation is unveiled.
The IS will drop it's value far quicker than the GS, as it's at the end of the model cycle and the GS is only at the beginning.