I think everyone agrees that just about all factory sound systems are "anemic" when it comes to mid bass and lower frequencies. Which is why I was asking what exactly you were trying to accomplish. So here's a few tips for ya:
1) Ipod in the aux input sucks. It just sounds flat. If you want to get the full sound out of your ipod, you need to use an interface like a Vaitech or even the OEM ipod interface. That will give you a USB input and the before and after sound just for that is a huge difference.
2) Pull the stock bass speaker and use an inline power amp for the sub and get a bigger better sub woofer with an adjustable low pass filter, and phase control. Suddenly it's a whole new system! You don't need to boost the bass so much now freeing up the other speakers to produce upper frequencies much cleaner now.
3) test all your exsisting speakers to make sure your getting a full sound stage and replace them. I've never said OEM speakers are great speakers, but if you use a different set that has a different sound characteristic, you might end up terrible sound. Also make sure the voice coils are ok, and the speaker suspension is still good and stiff. The reason I bring this up is you said it's an 06, so 4 or 5 years of banging the max line with the volume knob may have over stressed the speakers over time. Which results in a tired weak sounding speaker.