Spiralize the zucchini and yellow squash on the "spaghetti setting". Set aside.
To toast pine nuts, add to a small skillet over low-medium heat and toasted for 2-3 minutes.
In a large skillet, heat olive oil over medium heat. Add thinly sliced onion, garlic, and red pepper flakes. Cook down for 3-4 minutes until onions are translucent. Add snap peas and cook for 5 minutes. Add zucchini noodles to skillet and cook for 1-2 minutes until heated. Toss in lemon juice, basil, and toasted pine nuts. Serve immediately.