I've been driving current generation of Camry V6 XLE (a 30k vehicle .. I know I know..) but now that went out of warranty and gas was on rise so I decided to downsize..
so I bought this 2011 Elantra GLS + NAV (my Camry was opted with JBL) one of the biggest reason I added NAV was to get upgraded factory sound system.
it says 360 WATT but... man ... it's worse than my computer speakers. I miss my woofers.. it's the biggest enjoyment while in traffic or what not
maybe this is a payoff for downsizing? but come on now... worse than computer speakers? well that's my feedback on audio

anyone has good suggestion on aftermarket system? I'm not just looking for thumps but clear factory like sound.

Try speaker replacements, this site has an ok selection

http://www.parts-express.com/car-audio.cfm

the system on the new elantra with the nav is actually not bad.. i upgraded from an 05 mustang gt with the upgraded audio system which was a shaker 500 system with two 8" subs on the doors..

I must say the system on the elantra is pretty good for NOT USING subwoofers..

im sure if the speakers were replaced and subwoofers were installed would sound great but compared to lots of rentals I have been in and also my own mustang its not that bad..

you cant really compare computer speakers to the elantras... especially if you have a proper computer system.. surround with an integrated subwoofer system.

I added a sub to my 11 elantra and it sounds great

Add a small sub (10") and you will be happy. Most of the factory subs are 8" subs in the rear deck (no box) that offer filler base. A 10" in the trunk will be great for your needs.