You're not alone, these are issues that challenge all pizza makers. Here are some of my thoughts on the subject. First, fresh mozzarella is usually most at home on a true Neapolitan pie. Such pies are sparsely topped and cooked fast in extremely hot ovens. The high heat evaporates the moisture and the small amount of cheese used assures there so no excessive moisture. Some pies are just better when sparsely topped. A thin crust isn't the ideal platform for wet ingredients. I like to make thin crusted NY style pies which I seldom top with anything except cheese. Thicker pizzas can handle more toppings, but moisture can still cause the dough to be gummy. I like to roast peppers before using them as a topping. The roasted peppers can be lightly blotted with paper toweling to remove excess moisture before going on the pie. Mushrooms are tricky to deal with, as they are full of water. Some people like to precook the shrooms, others slice them very thinly. I'm not a big fan of onions on pizza, but when requested, I will finely dice my onions and they don't get overly wet on the dough. I will sometimes do the same with peppers, very fine dice still gives you great flavor and solves the problem of excessive moisture. Meats can also be slightly precooked to remove fat and moisture. Another trick some like, is to put a layer on cheese slices down on the dough before other toppings are added. The cheese forms a barrier between the dough and the wet ingredients. Just a matter of common sense. Sometimes, less is more. Adding more toppings then a dough can handle is not good pie.