Being an officer and pearlsack holder of a large and active linkshell, I can say from experience that there are many issues with the linkshell system that desperately need to be addressed. They include, but are not limited to, as follows:
1) This is an obvious one. Resolve the glitch that frequently (I'd estimate 50% of the time) causes the game to crash when the linkshell member list is opened. This should have been addressed long ago, there's really no excuse.
2) For the love of god, allow pearlsack holders and linkshell leaders to boot members from the linkshell without them being online. This is a very large inconvenience when you have inactive members and the only way to free up space in the linkshell is to break the shell and remake it entirely.
3) Make the linkshell member list more detailed. As in FFXI, display each member's current location, rank, physical level, etc. in addition to whether or not they are online.
4) /lsmes. We need it. Enough said.
Possibly more to come.