Well, fantastico is usually for people who have slow internet speed, if they want to install forum like vBulletin or phpBB, they need alot of time to upload. Therefore, fantastico was created for people who have slow internet speed or who is lazy and don't have time to install the scripts needed.
But the main point is,
1) Installing yourself has a higher possibility you may encounter problems, but it also notify u in the future if the problems occur.
2) Using the manual method, that is uploading the forum to the server, you may have some acknowledgement of how to do things, like installing scripts, forum, mods / hacks.
Using fantastico is more safer, but it doesn't update to the latest version. (Take note)
And using fantastico isn't that much of a troublesome needed.
Well, i personally prefer installing things myself.