I am picking up an 09 ls base with a aux port but no usb port

does this unit still play mp3s?

 

Yes you can plug an MP3 player into it. You can also play MP3 burned to CD's.

 

Actually I dont think the base stereo plays mp3 CDs, mine doesnt.
If the stereo has a CAT button it will.

 

can I just swap an upgraded factory radio in?

 

I have an 09 LS and have no issues with my aux port. I use a Sansa MP3 and works well. Also use CDs with all sorts of files and have no issues as well.

 

Hmm, perhaps they have changed since I got my '08, but there were three options for stereos, the base has no CAT button and wont play mp3 CDs, the mp3 stereo was ~$200 option (canadian), then the pioneer 7 speaker system was another ~$500 if I remember corectly.
All have the AUX jack though, so I use my cellphone plugged into it, works very well, just have to use the phone controls to change songs. Not a problem since my nokia has a remote on the cable to the stereo. Also works well to answer phone calls through the stereo.