For all the gnashing of teeth, once the smoke clears, minor league baseball will be a better product because there will be a higher concentration of legitimate prospects at each level. And in a sense, it's fairer to non-prospects, who'll know they're going to an independent league for fun before they start their "real life."
Now the quality of play at lower levels may be slightly worse (more talented but inexperienced players, fewer college seniors), but you'll have a better chance of seeing a future ML player.
I think one motivation was only partially money (I suspect with fewer MILB players teams will be more willing to increase wages and other support, it's easier to do so with 150 than 250 players), but also to stop the "arms race" where each team feels the need to have more minor league teams and prospects under control, no matter how marginal. This obviously favors the wealthy franchise where spending a few million more on minor league development is pocket change.