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Stephanie-

Most of the research into these drugs has aimed to address the issue of safety, especially when considering long-term use. This was of course made very difficult with the substance restrictions, but there's been a ton of research for the past 15 years or so (at least for MDMA, which is the only substance I'm talking about here).

The current trials are taking place because it seems at this point that there are no *extremely severe issues that arise from long term use. This is based on subjects that used MDMA, and these studies all have numerour problems (for example many of the subjects also used other drugs at some point, the studies aren't controlled experiments, etc.) The jury is still out on whether or not the physiological changes are "safe," especially when you're talking about long-term use. And to be honest I think it always will (the groups that want to find evidence that MDMA's physiological consequences are severe seem to find it, and vice versa for groups that expect moderate changes with effects that diminish over time).

Beyond the physiological consequences, the research that really made the strongest case for me was the article that examined consequences of MDMA use on cognitive functioning. They found deficits of verbal memory in heavy MDMA users compared to less-frequent users (<50 times!) and non-users. There were no significant differences in intelligence, attention, information processing speed, language, visual/spatial cognition, non-verbal memory, or execuitive functioning.  This suggests to me that while there is no consensus on the physiological changes, the cognitive changes are very minimal even with chronic use.

Back-Madruga, Boone, Chang, Grob, Lee, Nations, et al. (2003).  Neuropsychological effects of 3,4-methylenedioxymethamphetamine (MDMA or Ecstasy) in recreational users.  The Clinical Neuropsychologist.  17(4): 446-459.

I also think that it's very difficult to compare SSRIs to MDMA for PTSD treatment. Although SSRIs are prescribed to PTSD sufferes, they're not very effective. And more importantly, SSRIs are meant to be used daily for an indeterminable amount of time. MDMA however is only meant to be used a few times (maybe 2 or 3 times over the course of 1 year at most in a therapeutic setting). So although it does affect the seratonin system, the use would be incredibly infrequent. The idea with ecstasy is that its not any long-term physiological changes that are helping the patient over time (as with SSRIs), but rather the one or two instances changing the mental state that helps the patient get over major barriers they're facing so that they can deal with their issues better when they're in an un-altered mental state.

That said, I think your point of the mid-week withdrawal symptoms highlights another issue, as they may be more problematic in people suffering with disabling issues than the recreational population.