What is the best marinade? That's kind of a subjective thing. It all depends on what you like. With skirt steak, peppers & onions I assume you are doing the fajita type thing. If that is the case then a marinade of lime juice, oil, salt, chipotle pepper, cumin, ground coriander, and cilantro would be great. Or skip the peppers, caramelize the onions to top the steak that has been marinated in bourbon, honey, orange zest, dijon mustard, just a touch of cinnamon and a little cayenne, and then quickly grilled. Those are just two marinades you could make.