This is going to come down to what you want to get out of replacing your system. If you normally listen to talk radio at low volumes then keeping the factory amp, and figuring out how to send the low pass signal to it from the head unit is probably the most cost effective.
If you want good sound quality and higher volumes then ditch the factory amp and either use the on board amp in the head unit (good option) or put a dedicated amp to power your speakers (best option).
Speaking from experience, replacing those little in dash speakers is a waste of time and money. You'd be much better served getting a better quality set of door speakers that fit the factory location and just taking the in dash speakers out. They are really only good for high frequency and with them pointing at the floor they won't project the sound they are capable of making anywhere in the cab that you will hear benefit from them. The same is said for the rear roof mounted, unless you are in the third row they don't do any good.
In my opinion best option for something that looks clean and will produce good sound is dedicated amp for 4 door speakers, component speakers in each door, dedicated amp for subwoofer and 8-10" sub under front seat or fit in factory location with custom box.
Also remember car audio is one of those things that you get what you're willing to pay for. $119 for a set of 6 speakers seems too good to be true, so my guess is the speakers are pretty poor. A decent set of entry level speakers should run closer to $200 a pair. Stay away from big box stores and on-line deals and go talk to your local stereo shops. I've always found their prices to be competitive and they often have quality brands that you don't find at the bigger stores.
