"upgraded stereo" - you just pay more for more speakers. woo-hoo. If you want a 6-CD changer, just buy a 6-CD changer, and you'll have 7 CDs available at your disposal.
If you want the Homelink auto-dimming mirror, it can be added later.
If you want the anti-theft alarm system, it can be added later.
However, things like airbags, SE&SS/SKS, Navigation/voice control/Bluetooth, VSC, HIDs, cannot be added later.
Some people love the integrated Navigation. Some people detest it, and prefer a portable unit that they can transfer between cars and has breadcrumb capabilities and such.
On the Classic Prius, options were all a-la-carte. My mother ordered everything except for side air bags (not sure why), and the Navigation system ($1900 option, didn't come with Bluetooth or voice control yet, my mother didn't get it because of the price and she didn't know what its capabilities were, since no regular Prius were delivered to the US with it yet at that time). Now that she's heard others talk about the Navigation, and seen it in our 2004, she sorely regrets not ordering it. At least then she'd never get lost - she'd always know where she was. On the fly routing is great, although the maps are no better than mapquest/mapsonus/yahoomaps/etc. (As opposed to a bumper sticker her sister used to have: "I never get lost - everyone is always telling me where to go." ;-) )