A new Head unit is the 1st start to upgrading your stereo system....
This headunit will #1 amplify your speakers more than you car does....
#2 cleanup the sound quality IMMENSLY fromy a stock system and #3 add an extra kick of bass
Not to say you shouldnt get subwoofer in the future but a deck is by far the most important thing to upgrade first... it will be way better prepared to take furure upgrade like subs/amps/speaker.
May i suggest Alpines line of decks... they have a wonderful high quality line...
http://www.amazon.com/Alpine-CDA-9884-Dash-Radio-Player/dp/B0011E7U4I/ref=sr_1_8?ie=UTF8&s=electronics&qid=1230069105&sr=8-8 Would be a great option for you, and it is Ipod capable along with whatever other MP3 player you can think of "the aspect with ipod is that it can actually control an ipod via the headunit"
It is ready to have many upgrades easily added on so it would be a great option for you
Btw Dan where are you basing this from? beacuse you are wrong. speakers are deffinatly not the most important upgrade. and especially not a full set of speakers for under $200.