If it sounded good with the old speakers but bad with the new, the most logical source of the problem is either the speakers or their installation.
The Metra adapters are just wiring harnesses, so are not going to affect the bass unless something really bad is wrong and causing a near loss of signal. So unless the connections are barely made or the terminals are corroded they are not likely the problem. Switching the polarity will put the sound out of phase and could easily result in poor bass response. If left and right are phased differently you will also get odd sound imaging with a number of characteristics. It would be worth it to make sure you have both sides the same, just in case.
The first and probably easiest thing to do is to reverse the speaker wires. I would do the doors first and then the rears, since the doors seem to have the better bass response. Definitely don't do all four at the same time since that could confuse the results. If the sound gets better after the doors are switched do the rears and see what that change is since it is possible that one set is correct.
The new door speakers appear to have a higher impedance than the originals, and that will reduce the overall sound level, but should not reduce the sound quality. I have even been told that it will improve clarity, but haven't noticed that myself. My ear probably just isn't good enough.
Sky NA 2007 Midnight Blue
Sky RL 2008 Carbon Flash - Naked