Re: System Performane
This is really up to your needs.
If you focus on uncoded systems, you just look at the BER out of detector. For example, when you design a space-time code and want to see how much diversity the code can achieve, you look at uncoded BER.
If you study certain kind of channel code, Turbo code, LDPC, etc., you need to know how close your code is close to some limit, say the Shannon limit. Now you need to look at coded BER.
In practical systems, all are coded. However, in practice, at the receiver we have no access to the BER (otherwise you know the transmitting message already) and we usually measure the block error rate (BLER) through checking CRC code.