RIS (Roxen Internet Software) owns Pike, but this is likely to change in the not-so-distant future.
Too little documentation. One example is the lack of documentation about FastCGI support.
Webmasters like to use mod_rewrite in the .htaccess files to protect their sites from leeching, etc. Yes, there is referrerdeny and browserdeny, but these are accessible to the System Administrator, not the casual web user. On Apache, one can easily specify rules on a per directory basis. This isn't easy in Caudium, however, it is rare that someone would have more than two or three different conditions.
Now, for people that are running their own server, many of these issues disappear. Administration and adding servers is much easier. I'm not sure I agree with the templates, but perhaps an Apache Template could be tweaking beyond that to the System Administrator. In most cases, Apache has SSI turned on for shtml files -- getting the exec command enabled to mimic this in Caudium is not a task for the beginner. The maze of options to find that one setting will certainly frustrate anyone getting started.