There is actually a reason for every bit of markup that appears in ProcessWire's generated forms, whether from the admin, Form Builder or elsewhere (they are all using the same Inputfields system). Once you start removing things from it, you likewise remove some feature, capability or customizability from it. In some cases, you might even remove the possibility of supporting certain types of inputs.
That may be difficult to appreciate if you only look at it from the markup side, because it might be different from your own markup when making your own forms. Most notably, we have more wrapper elements and class names present than you would usually need in a standard HTML form. But these are not standard HTML forms, and you should avoid looking at it as such. ProcessWire forms have to cover more terrain than a typical web form. The Form Builder has to provide the capability of accommodating any type of layout, theme, or input (known and unknown, whether regular HTML or JS-based) with a common markup. Once you really start pushing Form Builder or ProcessWire forms, I think you can start to appreciate what the markup brings.
Creating a form is the primarily purpose of what a form builder is for. When you are creating your own form markup, then you are the form builder. So my advice is that when you want to use Form Builder, let it do what it is designed to do and it will perform beautifully for you. On the other hand, when outputting a specific markup is more important than the result, then don't use any kind of form builder. A form builder is by nature a markup generating tool aimed at giving you really powerful forms quickly. And ProcessWire Form Builder is an expert at what it does. But you have to trust it and let it do its job.
I've been both developing and using Form Builder for several months now, and strongly feel it is 100%. That's why I've moved it from beta to stable this last week. It is the most comprehensive and complete module ever built for ProcessWire (at least of those that I've built), including the core modules. Like mentioned above, you do have to use it in the way it is designed to be used and in the way it recommends. If you come across any issues or bugs that lead you to think some part is not 100%, then just let me know what it is -- I fix things very quickly. But I am not aware of any issues at present. At least, it is 100% stable with all the forms I am using it on at present.