I run 2.1 for that reason. I move every year, so getting the wires nice and concealed is either against apartment policy or too much of a pain in the butt for what its worth. Also, by concentrating on a 2.1 system, you can really put more money into fewer speakers, which helps quite a bit in the budget/entry-level/lower-mid-range speakers (up to 1500$ per pair imho).
The jump from 3 pairs of 200$ speakers to 1 pair of 600$ speakers in terms of audio quality can be quite immense if you audition and buy the right speakers. Granted it is a compromise for multichannel vs. stereo. If you listen to more music, I would suggest the 2.1 route. If you watch movies with friends, you have to do at least a 3.1 probably. If you really really cannot let go of surround effects, then 5.1-7.1 is what you have to do obviously.
Otherwise, people usually try to hide the wires beneath the rugs, or run them along the walls on the floor partially hidden by furnature. Rear speakers are always a pain, but if you have long enough speaker cable (with appropriate gauge) you can run them up, down, left, right, in, out until they are acceptable.