I think the woofers are fine. Just wondering if mine would be like your's and benefit from a higher quality woofer. I dont know anything about what is in there now and if it is a weak link like your's. My Prodigies seemed to have weak base but I figured out that AUdyssey had it turned way down I think, because my panels werent putting out much. Once I get the new panels in I should get more bass too I think. I use my depth i sub for most of the bass, but could probably use more "mid bass".The panels came from Martin Logan The Woofers were sourced from Parts Express ( Goldwood GW-12PC-4 12" Heavy Duty Woofer 4 Ohm ) The original woofers Eminence made for them are not manufactured anymore. They were not that good to begin with and were the designs weak link. The crossovers are external to the speakers and came with them. There were a couple of options depending on your setup at the time. More than likely your woofers can be re-coned if they are damaged. Just contact ML tech support. They will help you out.
The woofers in there now seem to be made of metal, im guessing aluminum?