I've always believed that the reason we use Balanced Field Length figures is that it simplifies calculation (as mentioned earler by A.Whittington) and also presentation.
In an airline with multiple destinations to airports with multiple runways - doing a detailed runway analysis for each and every combination of runways/temps/pressures etc would obviously be impractical.
Using a Balanced Field Length takes a 'Standard Runway' template and moves it from runway to runway where possible, thus avoiding multiple individual analyses.
This standard template is one which gives MAX performance (Max RTOW) from the aircraft at ISA conditions, and allows for corrections where necessary (temp/amb press/wind etc).
In the event a runway cannot give max RTOW using BFL then a specific analysis would have to be done.
As Mutt says, the catch (IMHO) arises when you put the BFL template for a small jet onto a 14,000' RWY. You may in fact then only be 'lookig at' the first few thousand foot of the runway (the BFL template) and you are potentially ignoring thousands of feet which are available beyond that.
This means that you could be led to believe you must make the V1 decision far earlier than actually possible in reality.
In current methods of presentation you often don't know if you are using BFL or not. Perhaps it would be a good idea if all Perf Charts had this annotated on the page?
By the way...all of the above could be utter bullcrap. I am simply stating my own (self deduced) understanding of the situation. Please correct me if I'm wrong.