Add the olive oil to a large pot over medium-high heat. Add the onions and cook until beginning to soften, about 5 minutes. Add the squash and peppers and cook, stirring occasionally, until just beginning to brown slightly, 5 to 7 minutes. Add the garlic and jalapeno and cook for 1 more minute. Add the broth, cumin, chili powder, salt and pepper. Bring to a simmer and simmer until the squash is soft, about 15 minutes. Puree using an immersion blender.
To serve immediately: Serve up in bowls and top with about 1 tablespoon each of the crema, cotija, cilantro and pomegranate seeds.
If freezing, let cool completely, then pour into 3 to 4 quart bags and freeze. To serve: thaw a bag of the soup in the refrigerator, then heat in a pan or in the microwave. Top with the crema, cotija, cilantro and pomegranate seeds.