You can get compact subs that fit behind the back seats or possibly even under the seat. I have a Cerwin Vega 10" compact in my car that sounds pretty nice. It's not going to give you chest pounding bass but it fills out the sound pretty well. IF you were going to replace the sub, you'd probably want to replace what's driving that sub as well since it's probably a limiting factor as well.

 

 

You may not want to splice into the factory wiring but that's probably gonna be your best option for sound quality and it wouldn't be all that hard. Even if you add a sub to the factory enclosure, the power output and the eq of the factory radio won't really give you much more output. The easy way is to just order a Metra harness to install a new radio, should be a 70-5520, maybe a 70-5522. What you do is unplug your factory radio, then plug in the metra harness. This will then tell you what all the factory wires are on the other side.

On the Metra harness the white/whiteblack and the gray/grayblack are the 2 front speaker wires. The purple/purpleblack and green/greenblack wires are the rear speakers. Use the front speaker wires as they will have a broader frequency range and will make the sub sound better.
Then you get a 2 channel hi/lo converter. It will have the same white and grey wires on one end and rca's on the other end. Using the Metra harness to guide you, tie the converter wires into the factory wires. Then unplug the Metra harness and plug your radio back in. You can then add a separate sub amp, amp power kit, and sub of your choice.

Kinda sounds complicated but actually pretty simple to do. Hi/lo converters are probably around $15 and you can probably get the harness off Ebay or Amazon for about $5-7. If you don't want to buy the harness just for the wire colors you can go to the 12v.com. it's a good place to get wiring info for stereos, remote starts and other things.