I can only imagine that most of you who are not having a great time with an ipad as a universal remote are using IR dongles rather than wifi to IR hardware units like the Global Cache stuff, or that you haven't used iRule. Or that you're really hard to please.
All of the problems listed above can be rectified with these two things - except the lack of physical buttons. I wouldn't be without my ipad / irule / gc wifi2ir setup. I have been able to put multiple remotes in a drawer and customise every aspect of my setup, with functionality that you can't get from the original remote (for example, with Air Control for the ATV2 plus iRule I can go straight to Netflix, or any other "app" on the ATV with one "button" press. Not a macro, - press down, press down, etc - I mean opening that "app" immediately.)
It really is worth investing some time in, if you have it.
(I don't work for iRule btw - I am just a very satisfied home theatre / home automation geek girl.)