I am not familiar with either machine, but to me the deal breaker would be if one has a needle up/down function. For FMQ, that is the most wonderful feature. Also, if you have the button start/stop, it can be useful. Some people hate it, but I find I can set the speed and start and stop sewing without the foot pedal. You have to get used to pushing the control to stop the machine, but your speed sure is consistent; another thing that makes for good FMQ stitching.
By the way - I have a Bernina 440 QE with the BSR and a Brother Innovia, and I use the Brother almost exclsively.