If you put on more aggressive pads you will be putting more energy into the rotor (aka heat) that it wasn't designed to handle. That said - you're right in that a big brake kit that doesn't add more thermal mass to the rotors will feel good once - and then on the second stop will be even worse than stock as the rotors overheat.
Alcon and Rotora use a thicker rotor (wider and more material) from what I can tell - so we can keep running 17" wheels. Powerstop and some others just put some fancy slots on an OE sized rotor and call it a day. ...but hey, the calipers look sexy right?
Good systems will use thicker rotors if they maintain wheel size, or larger diameter rotors if they mandate larger wheels. More thermal mass is required to improve longevity and absorb more heat energy. Putting on just bigger pads and calipers will actually be worse IMO. Your first hard stop feels good - your second (like in stop/go traffic or off-road) will likely be worse than OEM.