USL and MLS are two different organizations that are sanctioned by the United States Soccer Federation (USSF). The two organizations operate independent leagues from each other, so each has no jurisdiction over the other one's operations.
USL has teams in cities that MLS is not present in, but they are much smaller in scale... For example, the California Victory plays in the old Kezar Stadium (the ex-home of the SF Niners which was downsized after the team moved to Candlestick Park across town) in front of a few hundred spectators. I know other clubs have nicer facilities such as the Portland Timbers, but they are not as nice as Home Depot Center or BMO Field.
The most important reasons are money and marketability. To join MLS today, you need to pay a substantial franchise fee like $15 million+. For American sports leagues, it's an entry fee for a new team that gets distributed evenly to all the other clubs in the league. It would be hard for expansion teams to swallow if they get relegated to USL First Division after paying the big fee. Then you allow a club like the California Victory who paid a much much lower entry fee to get promoted... This doesn't excite current owners.
Marketability is a huge second reason and a reason why you have two conferences (East and West) instead of a single table system. It would be easy to allow the eight best-record clubs to make the playoffs, but what if all eight clubs are based in the East? Then no one on the West Coast would be interested in the playoffs.
Same thing applies to a relegation/promotion system in the USA. If both LA clubs stink and get relegated, then you have no MLS clubs in the second largest market in the USA (sounds like the NFL). This is not Europe or England, where the city of London has 13 professional clubs in its metro area with 5 clubs in EPL. Who cares if Fulham gets relegated (except for their supporters)... You still have Chelsea, Arsenal, West Ham and Tottenham to watch EPL in London. Even if you're hometown club gets relegated like Everton, you still can watch EPL at Liverpool (though I'm sure it won't be fun...)