Worth it to me for simplicity. Being able to wirelessly access my music, pictures and movies in one place with the ease that apple offers is very nice. I converted about 300 movies after I bought it but I looked at it like this... MP4 format is usually recognized by most operating systems. If for any reason I need to bypass the ATV and plug my HD into my samsung TV, all movies will be in a format that plays. Not sure that would be the case if I left everything in MKV format.
Simple and attractive formats for anyone visiting and looking through your library as well.
I was in the same boat as you in the beginning. I could do everything in some way or another...ATV just made it easier.