I'd just replace the radio, it really doesn't look too hard to replace when I skimmed through the docs. I replaced the radio in my old Saturn,
Crutchfield makes some great guides. and has the best tech support with very knowledgeable staff. Learning how to crimp and/or solder is really easy..
I'm considering buying one of those HD Tuner units for my aftermarket radio. If I take the time to replace my Yaris stereo, I might as well upgrade to HD radio as well. Pretty much the same amount of work, costs a little more though.
For $150 you should be able to get a decent receiver that plays MP3/AAC/WMA and has a couple pre-amped outputs so you can just plug tweeters or extra speakers into it if you want later. Another $100 on top of that, and you'll be tuning in XM (Satellite), SIRIUS (Satellite), or HD Broadcast Radio (free).
Not to mention that aftermarket receivers just look so much better and have a lot of cool features like built-in equalizers and such.
As much as I like my 2010 Yaris, the CD/MP3 player on it has an LCD screen that looks like it's from the 1980s and it really is an eyesore.