Alpha uses less steps to find a bookmark
Sort my folder means I have to go to that folder hoping I can remember which folder I placed a bookmark, then scrolling the that list to find my bookmark
Even if I was to create multiple folders I.e. Music, technology, financial, etc. Apple still not provide a way to alphabetized these folders either. IE has a simple Sort By Name item that takes 2 seconds to work and all my stuff is sorted/alphabetized for easy access and with a quick scan I know where everything is.
It's all personal preference. For how I use my bookmarks, alphabetical would never work. In fact, I personally find that the ones I have at the top, that show up in Bookmarks bar, are 98% of what I access. For the rest, saved bookmarks start coming up as I type things in Chrome.
However - I might have found a solution for you. Do you use Xmarks?
Xmarks | Bookmark Sync and Search I use it across all of my machines - it will keep your passwords in sync however you organize them. It's awesome. Their iPad app is free, but you have to be a Premium Subscriber to the service (which is $12 a year). I'm not a Premium subscriber because I use MobileMe instead, which syncs my bookmarks to my iPad and iPhone. But, if you don't have MobileMe, it's well worth the $12 to do a premium subscription. The caveat is that you'll launch your bookmarks from the Xmarks app, but they'll all be here.
On the alphabetical side, I've looked in both Chrome and Firefox on Mac (but should be same on PC)...they both have an option to sort alphabetically. So, you can set your bookmarks up alphabetically there, and use Xmarks iPad app (after you've installed it on your desktop to sync the data), and all of your alphabetically sorted bookmarks will be synced over to Xmarks iPad app.
If you have MobileMe, you can set it up to sync bookmarks on your desktop up to the service, then you turn on MobileMe bookmark syncing on your iPad, and you'll be able to sync the bookmarks right into Safari on the iPad (no need for Xmarks).
Let me know if other questions on how to do this...it takes a few steps to set it up, but once you do, you dont have to touch it anymore. If unclear - just let me know whether you are PC or Mac, whether you have MobileMe or not, and what browser you are using.