Most cruises have different types of rooms. Inside, Outside, Outside with balcony, and Mini-Suite (w/balcony). THen of course like you mentioned are the different decks. What deck you are on doesn't matter much unless you have a balcony type room and want to be higher to see further.
Only other difference than that is you have to walk less to get up to the top to eat and such, and it might be an extra 10 square feet in size at the very top.
Personally I always get the cheapest room I can get which is usually an Interior room on a lower deck). When you go on a cruise, the only time you are in your room is to sleep. I don't know why you'd want a hugehly expensive room so you can sleep in it. Most crusies (depending on where you are going) you will either be on deck most of the time or off the ship. But some people don't like smaller quarters in which case you need to shell out for the bigger room.
I did the Caribbean twice (inside rooms both times) and Alaska this July (inside room again). All of them because you won't be in your room much except to change clothes, go to bed, or to just catch a quick nap or something.
EDIT: As for pricing, travel agents can't usually get you discounts on things, but they can get you bonus like free upgrades, shipboard credits to use on the cruise, group discounts, etc...