With a 64-bit journaling filesystem, there are no headaches when dealing with large hard drives, nor is there such a high risk of losing data during a system outage. For starters, there's the lack of Java support in the Web browser. There are simply too many Web sites using Java today to allow any Web browser to be without support for the language. I had hoped for an alternative Web browser for BeOS, but alas, I was stuck with the pre-installed one. This will definitely be a problem if you plan on using your BeOS box to develop Web sites.
Applications are at present less than stellar, and that's being kind.
Marketing literature claims over 1,000 applications for BeOS and while this seems to be true, what is available is pretty primitive. If you're looking to compare BeOS to other operating systems, here is my two cents worth. Microsoft is simply ahead of the game when it comes to pre-packaged applications, although their base operating system is in my mind inferior to its competitors. And of course, BeOS will run on non-Apple hardware, making it far more accessible. And of course, everyone is comparing BeOS to Linux, which is an unfair fight, to say the least.