Well your research is correct, a Gamiviti would do every one of those functions you list above, including the jack, awning, lights and Thule accessories. The Thule cross bars and Subi towers aren't really going to help, other than you could sell them on CL to offset some of your new rack investment. Shoot me an email and we can nail down specific features, I'd be happy to work up a quote for you with any multitude of mild to wild options for a Gamiviti. sales @ gamiviti.com
With any rack, you want to remove the factory rack and upgrade the towers.. that factory stuff is just in your way and really not up to the future task at hand, particularly when you mention several hundred pounds. And with any rack, you need to either primer/paint it yourself if you get it unfinished, or you need to have it powder coated- really not an option to run it unfinished, yes rust is the issue.
As for decision criteria, your stuff above is a pretty good start. Other adders would be do you want a floor or not, do you want a bar across the sunroof or not, do you have a low clearance issue, and general functionality and compatibility with other aftermarket accessories, and just general appearance- your rack is probably the first thing you'll see every time you walk up to your truck, so my opinion is you should be really stoked with what it looks like. Obviously an opinion and a bit of vanity there, but shoot we're not driving 80 series anymore, no one's bolting up an ATV ramp here.