How to connect the pic16f59 to a pickit 3?
The description above is somewhat misleading. You say that Pin 14 of the Pic (Vpp/MCLR) is connected to Pin 1 of the PicKit3, which is OK. But then you say that Vpp of the Pic (which is the same Pin 14) is connected to 12V. Only one can be true.

Vpp/MCLR must be connected to the PicKit3, because it needs to control this voltage to properly enter programming mode. Also, the PIC16F59 needs a voltage between 12.5 and 13.5 volts here.

You also need to connect both Vdd pins (15+35) and GND pins (5+25) together (and use decoupling caps on both - 100nF should be enough).