As an owner of both JJP and Stern games I feel the main different is the passion being poured into code on a consistent basis. JJP over delivers on code and goes the extra mile whereas Stern does not consistently. It's great Stern puts 3-5 titles out a year but it also means a majority of their games will never have the code depth (not just number of modes but also variety, quality of choreography, etc) that JJP games always have.
Build quality wise I say both are fairly even. JJP games often feel built like a tank as they are using higher quality wood for the cabinet and the entire head itself is wood versus the metal / wood combo Stern heads use.
Finally I'll say that JJP games up until Wonka have had far more in them compared to Stern games. JJP seems to be going away from the crazy loaded games starting with Wonka.