Are you "simmering" or "boiling" the soup?
When preparing soup, especially from stock, anything above a very slow simmer is going to reduce the soup, so you end up with something that's more concentrated but - obviously - also much thicker.
What you should be seeing is just a few bubbles escaping to the surface every minute or so. That's it - that's all it takes to cook. If you're seeing more bubbles than that, you've got the heat turned up too high and your liquid is evaporating.
This doesn't answer your question directly, but spices are only a small part of the picture. Below are some techniques to get more flavor in your soup.
Longer Cooking
Depending on the type of soup you're making, you may just need more time. Some flavors just need more time to get out. This is especially true of meat and bones. It's possible to make a ham and pea soup in an hour, but simmer that ham for 3 hours and it's night and day.
Rest overnight
Many stews, chili, etc. seem taste "better" the next day. Give an overnight rest in the fridge a shot and see if the flavor improves.
Add volatile flavors later
There is a caveat to go along with longer cooking. Some items work over long cooking times, while others lose flavor. In addition to meat/bones, garlic, onion, bay leaves (and others) benefit. Many fresh herbs, pepper, vanilla, saffron (and others) lose their flavor from the heat. If you are cooking for a while, you might try adding some more volatile flavors later in the process.
Add salt early
Salt helps to extract flavors, so add it early on in the process. Do be judicious with it, however. Long cooking tends to concentrate flavors, so you can easily make it too salty.
Sweat vegetables / brown meat
Before getting any water involved, sweat your onions, celery, peppers, mushrooms, or whatever vegetables or playing in this game.
Likewise, brown your meat. The maillard reaction is necessary for developing great flavor from the meat.
Best Answer
Dilution is the solution to pollution.
There is no way to cover that smoke flavor. But you can thin out the Mexican soup with some other bland soup and that might turn out good. You could use tomato soup, or cheese soup or really any soup with flavors you think might be complemented by the Mexican soup. I am thinking clam chowder with smoky Mexican soup might be pretty good.
That said, I think some liquid smoke flavor is just bad. I never use it because I am scared of it. If the problem with the Mexican soup is not just too much smoke flavor but bad smoke flavor, throw out the soup. That bad smoke flavor comes out your pores after you eat it which is freaky.