The Prodigy is larger, and when I heard them last, I recall they had better bass extension, but not enough better that I wanted to pay for it.
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I have owned ML SL3's, Aeons, and Prodigy's. The SL3's are great speakers and I would not hesitate to recomend them (especially at used prices). The Aeons are about on par with the SL3's (actually I like the SL3's better), but the Prodigy's absolutely blow the others out of the water in every way....... then again they cost MUCH more. Be picky about your amplification and front end equipment to get the best out of any ML speakers though.
I recently sold my SL3's and went back to the box (Dunlavy SCIV-A). I was happy with the ML albeit I felt I needed more midrange and better bass. The soundstage and clarity of the ML SL3's are great but they need to be placed right to enjoy their potential. I have listened to the ascents and IMHO, was not different compared to the SL3's. The Prodigy's are in a different league--better bass, more clarity and the "plastic sound" of the lower models is not there, but the return is not that great with the step-up due to the huge difference in price.