I found this little tidbit in an interview with the director of FFXIV, and I thought you might find it interesting...
"Okay, uh, this time we have this, uh, called 'company' system, which is like advanced system of linkshell, which you will be able to level up as a group - as a whole - and, uh, we will...let you know more information shortly, so we can't disclose too much information at this moment, but also as a community tool people have this community website which you can still check out company status and your own character status so they will be able to enjoy the game even if you're offline of the game."
To me, it sounds like Linkshells are going to play a bigger part in the story, and will have it's own level of progression like how when you give a town gaurd crystals it raises your mission level, therefor giving you access to more missions. So, yeah, I think there are going to be Linkshell based activities along with it's own progression meter.
The website sounds cool too.