similar to what julio said, the main reason is that typical wheat-based noodles release a lot of starch into the water, which changes the consistency of the soup. the starches can add a dirty colour to the water, but more than that, they can also thicken the soup undesirably (think of making a roux). Finally, if there are leftovers, the noodles can sometimes become completely water logged, making eating it the next day a bit of a soggy experience.

That said, with all these considerations there are times when you might add the noodles directly in-- non-starchy noodles (eg. like rice noodles) seem to do ok. also parboiling regular pasta before hand seems to help a lot with the starch and can still help you achieve the flavour integration you mentioned.

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.