#1) You think that now but after flying a half dozen legs and/or IAP's to minimums day after day after day after day after day after day after day your attitude on the use of autopilot will change. I like to hand fly as much as the next guy but I also make good se of the autopilot. You'll see what I'm talking about someday.
#2) Autothrottles are an option most airlines don't take because they add weight, maintainence requirements, and simply aren't necessary. Many of the Challenger 604's have autothrottles installed, Cool toy - not all that necessary. #2B) Probably not fly by wire in the sense you're thinking of. The controls in the CRJ are actually connected to hydraulic power units at the control itsself that actually make the control move.
#3) Main gear doors would have no positives on the CRJ. They would add weight, increase drag, and add mechanical pieces that could fail.
#4) No - never. To add leading edge slats to the -200 would be a major, major undertaking. They'd have to redesign the wing and everything inside it. The inside of the wing has all kinds of things in it - anti-ice ducting, fuel tanks, hydraulic lines, etc,. etc, - all of those would have to be redesigned to a certain extent. It would be a looooong and expensive process. The -700 is the only updated -200 version you'll ever see.
#5) I don't know much about Skywest but I'll take a stab at it anyway. Not all airlines have the capital necessary to buy all jets - they're expensive. Not all airlines need -700s and -900s. Those jets are for "high yield"(more than 50 pax) long routes. And believe it or not - everybody brace yourself I'm about to make a sachreligious(sp??) comment - there are some missions that the mighty CRJ isn't perfectly suited for. There are some places that a turboprop can go and some things they can do that a jet can't.
Jason