Fantastico pros and cons

I always thought that Fantastico essentially just;

1. Placed a copy of WordPress on your server (not always the latest version, as you say, this is a local copy limited by the update frequency of Fantastico)
2. Set-up a database (and user) automatically
3. Configured wp-config.php accordingly

Then you’d just continue to use WordPress for maintenance as you would normally.

In the past, I’ve worked on WP sites that were set-up with it, and don’t recall any issues updating it.

Personally, being a geek, I always run a manual install. Just feels cleaner, plus I know I’m always starting with the latest and greatest version.