Any organization you create manually in the manage favorites will be retained, since you are reorganizing an html file, you can drag and drop items in the favorites manager, but there isn't a native way to alphabetize them that I know of.
Each browser has made a choice of how to do favorites, each with some pluses and minuses, IE has separate files for each favorite, which strikes me as a very inefficient method, and very hard to deal with, Firefox uses html, from the netscape days, which I like since it's an actual file I can look at, Opera if I remember right uses some kind of little database file, proprietary format. It just comes down to what you want.
Can't speak to much for stability, don't use Opera except for testing, but seems pretty stable, solid, although now that I think of it I do remember some of the 7x ones crashing for no apparent reason. It's accurate at rendering until you get into the more advanced CSS stuff, then it starts failing, the size of the rendering engine just can't handle certain situations from what I've seen, but that's not really what it's made to do either, its main market is handheld devices, and they have to make sure the package works solidly for that, which it does, it's fantastic.
However, the kinds of errors I see in Opera will not affect 99.99% of the webpages out there, although they are annoying when I do advanced CSS stuff, I can always count on errors, at least one, sometimes more, in Opera. But that's advanced CSS, not a super important real world issue.
Firefox gives me the piece of mind knowing that almost any CSS I try to use will work without headaches. And that I can add and remove features at will, experiment, play with it, test stuff, dump stuff, it's a different concept. Most of the extensions would take only a few seconds to download, they are very small, often only 10kB or so. If you want the ready to go all in one package and don't need the extra power gecko/firefox has, then Opera is a great choice.
The choice of having a pretty lean, stripped down but highly configurable browser like Firefox versus a feature packed package like Opera is exactly that, a choice. The ability to have this choice is absolutely fantastic, only 5 years ago this was not an obvious outcome to the browser game.
Opera could help themselves significantly in terms of gaining market share if they would understand that the price they charge is too high, they'd make more money if they cut it in half, or better, to around $10, I'd bet the extra sales would make up for the difference.
Even with the ads minimized I still see it, and it's annoying, I don't want to see anything at all in my toolbars but tools/menus, but I'm not going to pay that much for a browser, and neither will most other web users. This is the main reason I believe they have had trouble growing their realworld market share.