My mids are pretty much just installed in the door's 6 1/2 cutout. I can understand that contributing to the speaker's lack of punch, but how does that contribute to its muffled sound. To me, that sounds purely like some sort of deficiency with the speaker itself.
Backwaves, lobing, baffle step, diffraction artifacts, off-axis alignment, phasing, etc, etc, etc.
I'm not trying to be a smart ***, but how many home audio speakers have you ever seen that are just mounted to a metal ring?? Car audio vendors haven't figured out how to defy physics yet, and are still constrained by the same factors that home audio vendors are subject to.
That being said, you're best bet is to treat your doors to a good healthy dose of deadening product. Then use an MDF baffle to help lower resonance even further. Seal up the mounting plane so the back of the speaker is isolated from the front, eliminating backwaves.
Figure out how off-axis your door speaker are. That's the degree to which they are facing away from you. This will affect upper midrange response greatly and needs to be highly considered when choosing component sets.
I'll stop there. You may actually not like the JLs even after all this, but there's not a speaker out there that will behave well mounted in a stock location, with no prior treatment.