If while rooted you change something that a stock update will conflict with, the phone will brick. What can that be? Thousands of things in hundreds of files. That's why the update checks for root (among other things) and is supposed to "fail" if the phone is, or has ever been, rooted.
So, no, there's no way to do a stock update to a rooted phone and be sure that it won't brick. Do a full update, make sure you have a stock (or rooted) ROM to flash to the phone, try the update, if it doesn't work (because th phone is rooted) unroot and try again. If it still fails, you'll have to flash the stock ROM - even rooted, the phone shows signs of having been rooted once.
If the update bricks the phone, you can flash the stock ROM, update, then root (if there's a root method for the version you update to).
As far as the best ROM, that's like the best flavor of ice cream. There's no ROM that's best at everything. Do you want more control over the user interface? More control over the CPU speed? A faster ROM? One that uses less battery (which will probably be slower)? The best ROM - for you - is the one that does what you want, and doesn't do what you don't want. If the stock ROM does what you want and doesn't do what you don't want (there are a lot of things you can do with apps - you don't need a different ROM just to, say, get rid of TouchWiz), that's the best one for you.