Is there a reason for the choice of E.coli as a model for many bacterial systems? Other bacteria such as B.subtilis are also used, but why is E. coli preferred?
Short answer. It was discovered pretty early (late 1800's). It is easy to get (you probably know where it comes from), purify, grow and is not virulent. E.coli spreads very rapidly (30 minutes division rate).
Why this one in particular and not another similar bacteria? Well you have to choose something at some stage and usually the more an organism is used the most valuable it becomes which means that more and more scientists will start to use it creating a loop which favors certain organisms, like it happened with E.coli.
E.coli started to be studied because Theodor Escherich wanted to prove the "germ theory of disease" which led him and later other scientists to work with E.coli and everybody uses it today.
By the way, the mouse model is actually quite interesting. Started by breeding huge amount of mice for selling them as pets.