I don't consider either the transponder failure, or the communication failure to be very important factors in this accident. Transponders and radios do sometimes fail.
In some situations, an aircraft can be allowed to takeoff without a functioning transponder and/or TCAS system. There are many examples of this.
Temporary loss of communications are EVERYDAY occurrences all over the world. Many things can cause this. It can be as simple as the pilot turning the volume too low. An earpiece falling out of your ear. Stuck microphone blocking transmissions. Out of range stations. It happens every day. In fact it probably happens on every flight.
An ATC system must be designed to be failsafe. This is not the case in Brazil