There's a few types of salsa -- salsa fresca (aka pico de gallo, aka salsa cruda), which is "fresh salsa" and uncooked, and if made fresh, it shouldn't be too watery (unless you add to much liquid, eg, lime juice), but letting the vegetables sit after salting will start to draw out extra liquid and could become watery.
For truly thick salsa, you have to treat it like a jam, and cook it to release the pectin in the tomato. (or I guess you could use some other thickeners ... I've never tried. tomato paste, maybe?) You don't necessarily have to cook the other ingredients, too, but I personally like roasting the peppers and onions to sweeten then up and remove some of the extra liquid. (halve the peppers and seed them, lay them on a tray cut side up with the onion cut into wedges, roast 'til they're softened, then dump into a food processor and either pulse or liquify it, depending on how chunky you like it. And the skin falls off the peppers, so I leave 'em out).
You can do the same roasting with the tomatoes, and it'll be thicker from the food processor, but you won't get the same cling without letting them cook slowly in liquid to develop the pectin. If you roast the tomatoes, I like to use plum tomatoes, as they have more "meat" to the gel around the seeds, and take out the gel and seeds.
My guess would be that you boiled the soup at some point, possibly for an extended period of time.
If you bring it to a full boil the fat from the meat will emulsify and distribute itself through the liquid. This is the same stuff that foams to the top, the "scum" that a lot of recipes (usually ones that say bring to a boil, then simmer) tell you to skim off. I would venture to say that this distribution of the fat into the liquid is also why it tasted heavier.
When making stock or soups, the most I'll heat them is to just below boiling and keep them at that simmer for a little longer to make up for not bringing it to a boil. When making stock, I strain once through a chinois and again through a piece of cheesecloth in a chinois to help reduce the floating particulates, but this won't really solve the cloudiness problem (though it will help some).
You can also try putting it into the fridge overnight so that the fat comes to the top and solidifies, but I don't think this will solve the problem, only help reduce it.
If it's just the stock that's gone cloudy, this page has some suggestions on how to clarify it, but honestly unless you're presenting it to guests, I see no reason to even bother. I've made cloudy stock and clear stock before and except for a slight "heaviness" difference, the taste is generally about the same. The cloudy stock sometimes has a more oily mouth feel, but it's not a major difference - and I've found some people seem to prefer the soups or rices I make with a cloudy stock.
If you have a hard time controlling the temperature on your range-top, you can use an oven-safe stock pot and cook it in the oven at 180°F to keep it just below a boil.
One other trick, depending on what kind of soup you were making - if you were making (for example) chicken soup, consider trying to turn it into a cream of chicken soup to hide the cloudy broth :)
Best Answer
Fennel is a fairly delicate flavor. I can see how caramelized onion and tomato would easily over power it. The bulb actually provide the most delicate flavor of fennel. If you want a more pronounced flavor, I would suggest fennel seed. I would further suggest you toast them first. They can then be used whole, or, if you want an even stronger flavor, grind the seeds. You could also garnish with the frond, but still that is rather delicate compared to using seeds.