I will probably state some obvious things as i go
I haven't used that specific pioneer, but i've used many others over the years and I like the simplicity. Flashier head units are more likely to attract thieves as well. I use a DEH-P6000UB. If you intend to add amps for all speakers try and get one that has 3 preamp outputs.
Polk speakers are good, You can find them in many sizes and power ranges. I have some high end that require more power. If you don't intend to amp the speakers aim for their lower power rated ones (35WRMS and less). Marine rated is a perk, but you want to use something like electrical contact silicone on the back to prevent water getting behind your dash and shorting the leads together.
Sub all depends on preferences. There are some good console ones that will keep it close to help with road noise/top off. SirGCal's website
has some info on putting 1 sub in the back seat. This will allow you to get a bit bigger sub with more power, plus downfiring to cope with the top down.
I personally built a box for 2 10's behind my back seat, amps below the seat. I have plenty of power to beat road noise on the interstate with the top and doors off. These of course are downfiring as well.
I've heard of people getting 2 12's to fit but i've never actually seen it done. I would also avoid "truck boxes" that will have the sub facing your back seat as the seat will absorb and deflect all the bass when the top is off.