I'm assuming you are equipped with a factory external amp? If you are, I'd do all 4 speakers first (on a budget).
If no amp, I'd do the HU + speakers at the same time. This stuff isn't that expensive anymore. With just the stock HU running your aftermarket speakers the difference won't be that large. If really constrained for cash, do all 4 speakers. Then look to do the HU after or (Vice/Versa, HU then speakers).
I do agree, all the factory equipment is junk. You won't be satisfied unless you replace it all. Will need a good HU, 4 speakers, a sub and amp for good sound. I laughed when I saw a couple ads for the stock stuff being for sale, then I saw that some of it had been sold! Yes, some people aren't as picky and the factory equipment sounding as good as an Ipod dock with 3" speakers is good enough for some.