First off, eBay is your friend… you can get some really nice stuff for a whole heap cheaper than if you bought from West Marine, Overtons, Crutchfield, etc…
Go with at least 6.5" speakers–there’s a ton out there to choose from in every price range. If you have room, go for 6x9… it really makes a big difference. Since you’re not planning on running an amp, you probably don’t need to go high-end like with stuff like Memphis or JL audio. I’ve got a pair of infinity marine 6x9’s ($100 shipped) on the side of mu console (runing from a 60x2 JBL amp) that I am extremely satisfied with, but I’ve heard similar speakers running off the head unit and they sound good as well.
Smaller speakers are not necessarily going to be quieter than bigger ones as much as they will not produce as low of frenquencies, which means puny sound.
As far as the stereo goes, I have really enjoyed the two Clarion I’ve had (first one died when boat got, ahem swampped), and I had it pushing 4 5.25" speakers, which it did well (17W RMS, 50W peak).& I could hear it while running. Plus, the sound quality was better than some of the other units I’ve heard.
I just bought a splashproof Clarion CMD4 (old model, refurb) for a buddy of mine for $140 shipped off eBay, and I’ve got a Clarion M455 (Same guts basically, not splashproof) that I paid $100 for. They do not have USB ports, but both have AUX IN, which makes it easy to connect anything from an iPod to a cell phone with .MP3 capability.
I’m not up with what is super new, but I can’t recall a marine radio with a USB port, and it seems like the USB port itself would be a weak point for water to seep in and fry the whole thing. Fusion makes a radio with a built in waterproof iPod slot, but it’s quite pricy.
As far as speaker placement goes, if you really want to hear it while running, I’d put two on the side of the console and two facing back. You won’t be able to hear the front ones as well while running, and my side-mounted speakers fill the boat with sound well (mounted