The tactical manner to handle a Uber is to retreat. This doesn't mean you have to move away from objectives you're protecting, but you need to make it so you're no longer a temptation for that uber to take out. Specific classes have abilities against the Uber now, as well as the patient whom is being Ubered. Pyros, for some reason, seem to be easily thrown into the air by projectiles, and even though they take no damage from it, they are momentarily thrown skyward and lose their forward momentum, giving other players more time to escape taking damage.
Pyros, on the defense of an Uber, can use the compression blast, like Demo Sticky grenades, in an attempt to separate the Medic from his patient, or harass them for the duration with multiple puffs of air. The gameplay mechanics of the Uber, on the otherhand, of rather numerous.
The shiny color coating easily itentifies not only the fact that there is an uber, but indicates which team initiated it. The Medics vocal indication of a full ubercharge is an audio cue to his patient that one is available, however, it also indicates to nearby enemies to take refuge, or flush out the pair to be killed before it can be deployed. The Patient automatically thanks the Medic when the beam is pulled off them as another audio cue to the Medic/Patient that the beam has been disengaged, and is accompanied by the blinking uber skin as a visual cue to the patient that they are going to lose the benefit of the uber.
Where this Uber succeeds, IMO, the Krit-Uber fails. The effect of the Krit-Uber, on the weapon of the Medic/Patient as well as the pulsating charge particles in the beam is NOT as easy to discern when the uber has been popped. People are more focused on the large shiny crit weapons fire coming from the patient than to easily be informed that the Medic had initiated the Krit-Uber. If the charge lightning effects were much larger, perhaps sparkling all over the character models in team colors, this may prove as a better indication that the Krit Uber was in effect.