The cars can run on regular gas, the engine just retards timing (lowering performance) to accomidate, and prevent damage. As the price difference is about $.20/gallon and you'll likely go 15,000 miles/year, you're looking at $200 extra in fuel costs. Pretty irrelevant on a $20,000 car, especially when it decreases performance.
Many people feel that an automatic takes some of the fun out of the car. The CVT on the MC is not a normal automatic, and if you check some of the info in the CVT forum, you'll find out it has a few nice benefits. As the S automatic is a normal automatic, and has just become available, its difficult to say how well it will perform, but of course MINI's advertisements for it seem to make it sound like the best thing ever.
If not knowing how to drive a manual is part of the concern for picking an automatic, there's plenty of people who have bought MINIs and learned to drive a standard on them. Of course if there's other issues, like a bad leg or insane traffic, that's a big benefit of the auto.
it may make sense to look at your option packages to choose between the two, an MC with the sport package and a few options starts to become near the same price as a base MCS which has 16" wheels and the stiffer suspension included.
Finally, the only option people ever really, really wish the had bought is the multi-function steering wheel. Every other option some people think isn't worth it, and others think it is. some of course don't think the MFSW is worth it, but they're usually a small minority. Beyond that, its personal taste and preference - do you want a simple basic car, or would you prefer some options, its really up to you. In the US (where I assume you are) many people get sport, premium and cold weather packages, but maybe your budget doesn't allow that, its individual taste really.
Color is dependant on personal preference, its common to give up color to get a car faster, which is usually easy because most people like most of the colors. I'm not sure someone who was planning on a silver car would suddenly want a yellow one though, that's a personal taste issue.
If you get HK adding a stereo aftermarket is a pain, because you need to remove the entire HK system, or interface with the amplifier for it, neither is easy. If you don't get HK, its easy (if you have someone who knows what they're doing with a MINI) to remove the stock stereo, and upgrade anything you want - essentially, decide if you think the HK is good enough, if its not, don't get it and go aftermarket entirely.
Unlike a Prius, you'll get good milage on either car on the highway. Its reasonable to get in the mid 30s on a long drive on an MC, or in the low 30s in an MCS. sure its not prius level, but its way better then most other cars with the exception of the VW diesels.
Stay away from Demo Cars! Everyone drives them like they stole them, and rightfully so. You test it because its not your own car, you do what you'd never do with your own. Its a bad idea, and not worth saving the wait time. Call around to other dealerships, and see if they have something new in stock, or coming in on the boat. Get a brand new car, treat it nicely, and it will reward you. You just can't do that with a Demo because for the first 2,000 miles, 100 people drove it and thrashed it.
The Chrono pack is a nice idea, implemented not very well. It doesn't seem to look right, and seems to mostly be an excuse to get the speedometer in front of the steering wheel, without spending $1700 for the navigation system. If this is your main car, you'll get used to the center speedo in a few weeks, and its a unique part of the MINI - no real reason to get the chrono pack. Save your money for options you want, like the chrome
