What are the limiting factors for high altitude planes (e.g: U2 or SR71) preventing them from going higher?
The limiting factor for subsonic aircraft, including the U-2, is well explained here.

For supersonic aircraft this answer simply says the limit is "a combination of wing loading and maximum speed". If you look at the flight envelope of the SR-71 below, it becomes clear that more altitude can be best bought with more speed.



SR-71 flight envelope (picture source). Tower buzzing at Mach 3 is clearly impossible.

Supersonic speed limits


Intake design: If the kinetic energy of the flow cannot be efficiently converted into pressure in the intake, thrust will suffer and will drop when the flight Mach number is increased beyond the limits of the intake. 
Airframe efficiency: If the leading edge sweep of flight surfaces is not high enough to keep those leading edges within the Mach cone, drag will rise and limit the top speed of a design. The desire to reach Mach 2+ speeds was the driver for the many swing wing designs of the 1960s.
Compressed gas temperature: Once the compression heating in the intake brings the gas temperature close to its dissociation temperature, the chemical energy in the fuel cannot be fully converted into heat. This reduces engine efficiency and is the reason for supersonic combustion in designs for speeds in excess of Mach 4 or 5.
Aerodynamic heating: Metals and composites show decreasing strength with increased temperature. Fly fast enough for some time, and the structure cannot tolerate the flight loads, even if dynamic pressure is kept constant.


The order in which I listed those limits ranks them with increasing speed. Once you move beyond Mach 1.6, every consecutive tenth of the top flight Mach number must be bought with increasing expenses and compromises. Going beyond Mach 5 with current technology will only be possible with rockets, so those designs quickly become low-orbit satellites. In the end, it is simply not worth it to push the limit yet further.



EDIT: It seems the answer is not explicit enough. If we try a thought experiment and modify the SR-71 to reach higher altitudes, the possible options are:


Just pull on the stick: This helps in the short term, but flying stationary at lower density would require a higher lift coefficient and a higher angle of attack. This would lower the overall L/D of the plane and slow it down because the engines could not develop sufficient thrust.
Increase engine thrust: This could be tried in flight by advancing the throttles at top speed, and the aircraft would accelerate. This would quickly exceed the limit of the compressor inlet temperature, though, leading to a shorter life time or even damage of the engine's hot section. Next, range would suffer due to the higher fuel consumption. If the engine is improved by using better materials, a moderate increase in cruise Mach and, consequently, flight altitude is possible.
Lower wing loading: A lighter aircraft can cruise at a lower density, all other parameters being equal. At the end of a trip the SR-71 could reach the highest altitude, just like any other plane. Structural changes to lighten the structure beyond removal of all reconnaissance equipment, however, would have only limited potential: The SR-71 was already designed efficiently, so there is very little potential for weight savings without compromising structural strength. And removing the cameras and side-looking radars would strip the plane of its operational value.