macosSecurity
Whenever I open an application not downloaded from the App store (or a trusted vendor) I get a warning.
The warning reminds me a bit of the awful window popup that comes up every time you want to open an executable that says something to the effect "are you really sure you want to open this?".
What else about Mountain Lion makes it more security conscious?
Order now. You'll get Mountain Lion free no matter what, and it's a pretty painless process to install, particularly on a clean computer.
It's probably a toss-up whether you'll get Moutain Lion or not. It seems likely that it will be released before the end of the month, but when that image gets pushed to machines is anyone's guess. And even if you do end up with Lion, that may be a blessing in that you can wait out any 1.0 bugs if they pop up.
Ordering now gets you in the queue, and there's virtually no downside to not having a copy pre-installed.
To answer the question in your update "Can Time Machine do selective restoring?", Migration Assistant (in /Applications/Utilities) can restore data from a Time Machine backup, with some control over what is restored. See Apple's HT4889 for some details.
You also asked: "If I restore my entire home folder, will I also be restoring the faulty settings related to the crashing apps?", sadly, yes this is a possibility.
"Can I recover selective apps from Time Machine?" I don't think so.
Best Answer
Apple computers have long been considered "virus free" although Apple stopped pushing this as a selling point earlier this year in the wake of several Apple targeted viruses. The truth is that a virus can be programmed for mac much like a software application can, the reason for the lack if infections on mac was merely the same as the reason for lack of some apps in the past, the relative unpopularity vs windows machines meant it was less practical to program for mac. With macs now being more popular than ever before, Apple now has to implement strict measures to hold on to their clean, virus free image, hence Gatekeeper being added to Mountain Lion.