Not asking for Letter of Recommendation from Masters thesis supervisor
It will look a bit weird, yes. And the other faculty members in your department probably do not know you as well as your thesis supervisor, so their letters of recommendation will not be very specific. But I've never seen this be reason for an immediate rejection, which means you can make up for it in the rest of your application.

Probably an unnecessary tip, but: don't express your dissatisfaction with your supervisor in your applications.