ESP-12F Schematic Diagram
This is a simple circuit for ESP8266 chip and can be modified more,
First of all let's answer your questions:
1- 10K is a normal pull resistor for designers, but if your system is very sensitive on current drawn, or your system is battery powered, it's better to increase pull-up resistor to reduce power consumption while key pressed or I2C transmission.
2- It's very necessary to add decoupling capacitor/s, it's reduce L (Inductance) of power line and also suspends noise that digital systems make and better stability. Remember to use ceramic capacitor, when electrolyth Caps are have inside L that's not good for decoupling.
3- In case of programming, there's much more current drawn by chip, so it's a clever idea to use external power for programming, but it can cause voltage problem if you connect two power source together, to prevent this, add a slider key or jumper to prevent this problem.
As another suggestions, I recommend to add a capacitor to boot and reset pin and to ground for more stability and reset debouncing and prevent noise on reset pin.