It also gives the clubs a "fair" way to divide up the soccer talent that's not come through their various youth academies without going through the hassle and expense of a bidding war over every decent talent that shows up in the American college soccer system without participating in an MLS academy--which is still a heck of a lot of players.

You have to remember that the biggest threat to the success of soccer in America (at least in the minds of the people running MLS and I would argue that they're not wrong) is the league bankrupting itself. Almost all of the league's goofy mechanisms are geared towards assuaging this one fear in one way or another. The SuperDraft isn't exactly integral to keeping the league under tight financial wraps, but it helps. Look at England where they're throwing out tens of millions dollars all the time on hot young prospects many of whom never pan out. You can have that in England because most of the teams have ridiculously deep pockets, but in the MLS having even 1/10th of that problem could be fatal to the league's solvency or result in a situation where the LA Galaxy or NYCFC win everything every year because they're the only teams that can afford to compete for talent.