I'm a DLR vet, but I do love Space at Magic Kingdom (actually there are some really neat things at MK!) I was disappointed when MK didn't get the major refurb that was planned. DL's definitely made the ride smoother and better.
I think the original problem isn't just that they shortened Space's refurb at MK, but that whatever changes they did make to the ride made the ride worse (as in, more painful) than it was before. So now they've gone in and tried to remedy the problem, and most likely the only way they can afford right now is by installing trim brakes.
What they probably really need is to re-profile certain sections of track to eliminate the jostling that the 2009 refurb caused, but they can't afford to do so. (Or perhaps just don't want to fund the expense.)
The positive thing is that at least WDW knows there's a problem in the mountain big enough to necessitate money and attention. The negative thing is that, at least right now, judging by some of the above comments, the chosen solution dampens the ride experience by slowing down the rockets during key parts of the ride when they are supposed to be moving faster--and originally did move faster, more comfortably, before the 2009 refurb.
Maybe it will help WDW finally realize that Space still needs that major refurb. Time will tell, I guess.