Bring a large pot of salted water to a boil. Add the penne pasta and cook according to package instructions until al dente—usually about 10-12 minutes. Once cooked, drain the pasta, reserving about ½ cup of pasta water, and set aside.
While the pasta cooks, pat the shrimp dry with paper towels. In a medium bowl, toss the shrimp with olive oil, chipotle powder, garlic powder, salt, black pepper, lime zest, and half of the lime juice. Let it marinate for 5-10 minutes to soak up all those vibrant flavors.
Heat a large skillet over medium-high heat. Add the marinated shrimp in a single layer. Cook for about 2-3 minutes on each side or until shrimp turn pink and opaque. Remove shrimp from the skillet and set aside.
In the same skillet, add the diced red onion and sauté for 2 minutes until softened. Toss in the cherry tomatoes and cook for another 2 minutes until they start to soften. Add the cooked penne pasta, shrimp, and the remaining lime juice to the skillet. Stir everything together, adding reserved pasta water a little at a time to loosen the sauce if needed.
Remove from heat and sprinkle chopped cilantro over the top. Give everything a gentle toss once more, then serve immediately. For an extra touch, you can add a wedge of lime on the side for squeezing over the dish.