The brand / choice on speakers is largely subjective, so long as its not a crap brand like pyle or something, get whatever sounds good to your ears. Preferably from a place that lets you test the speakers on a wall so you can hear the differences.
From a strictly audiophile perspective, round speakers are superior to elliptical, however the elliptical speaker will have more surface area, and will move more air for a more bassy bass, and the difference in audio quality is not something i have ever been able to hear.i would go with the 6x9 speakers, unless the speakers you want to use do not come in that size.
The previous post to this one is right, the speakers are the single best audio upgrade you can make, i would argue that the next is the deck (radio) and then depending on what you like to listen to, and how you like to listen to it, a small 4 channel amp or a sub woofer to fill in the lows.
The bose amps are junk, i have literally bypassed them with just a radio to the new speakers and no amplification and had customers completely stoked with the improvement in audio quality. If you want to replace the bose amp with something similar in size but much better, a power pack like the apline or kicker units is a good option at a pretty low price. They use a lot less power than a full size amp and deliver almost as much output power, way more than most people need or want. The power packs can also be hidden behind the dash in most cases instead of under a seat or on the back wall of the truck.
Lastly, the front speakers are 95% of your sound quality and power, you could leave the rears disconnected and probably not notice from the front seat, so spend your money on the fronts, and do whatever with the rears. If you are going to amplify them though, they need to be replaced. The factory, even bose speakers are not capable of taking more than 10-15 watts RMS on a good day, at least not for very long.
And just to throw this in there, if you have the options between 2 and 4 ohm speakers, i would go with 4 ohms. While its true you will get twice the power out of the 2 ohm speaker, this amounts to only a 3 db increase in the output of the speaker, which is barely enough to be detected by the human ear. However it does double the power consumption of the amp, and the power going through the speakers coil(s) and will make everything run much hotter for really no reason. The only time i would recommend 2 ohms is if you were trying to get it as loud as possible on a budget with basically no other considerations besides LOUD. Some radios may also go into protect mode, or may not be able to handle the power demands of a 2 ohm speaker. in this situation an amplifier would be required to run the speakers.