Hi,
Don't worry about beta, we all have these "time" problem as developer, this is fine, don't feel bad about it.
I don't think it's realistic to build any game that has more thousands of gameObjects ACTIVE at a time. It's clearly a alert that optimization at the core of the application is required. you should always optimize this and at the very least disable all gameObjects and fsm not currently active.
Can you tell me more about them 1,000-10,000 fsm? is it elements in your scene, players? ennemies? at a given time, a layer only have so much gui element on screen, 200 elements is already A LOT, that is including layout gameObject etc etc. one way to optimize this is to have less items per screen and some menus and wizard to take a more discrete approach to gui.
Same with actual content, "active" content should always be kept minimal, you can't really expect 1000 ennemies running and firing after you isn't it? You may have 10,000 objects in your projects globally, but they will likely not be all active/loaded at a given time.
Also, bare in mind that it may slow down during editing, but the only true performance test must be done when published. Even Unity own interface dramatically slow down perfs, PLayMaker editing interface is no exceptions. When running, PlayMaker is nothing less than c# all the way and will be just as efficient as any other frameworks in place. It will have an impact because more classes and variables are used to run the framework, but it's clearly incomparable to what you experience during editing.
bye,
Jean