Well in Triple Spark we have scheduled event days (twice a week currently), where we try and fit in all those who show up. Of course as we have a DKP system everyone in the LS is encouraged to come and so if we have 9+ priority for spots has to go to who is needed by the current strategy (meaning a main tank, and x # of mages), who still needs items, and finally who simply wants to go along. Overall we try not to have too many people sitting out, because the truth is there is no good solution to that problem.
For people who want to do darkhold more than twice a week like those in our LS with all classes to 50 and nothing better to do, we run pick up groups at other times.
I'd personally hate to be in a linkshell with a "first string" group. It is really very hard to have a roster capable of supporting multiple balanced groups, not set groups (cliques), but completely interchangeable ones I guess that would be the ideal goal. It is just very hard to pull off because you need to have extremely carefully balanced recruiting or you'll be left with more problems than being under-full.
We have aimed at being a more traditional "endgame" linkshell since launch, however XIV's development cycle hasn't really lent itself to that (still not having alliance content, and going from 15-8 person parties). As a result we are forced to be a relatively small LS compared to most which brings with it its own problems (we struggled for a long time with a shortage of mages after a few key members quit the game); but on the other hand we don't have cliques, have little drama, and have a roster full of I think reliable people most of whom have been with us for a long time.
Our real goal I think is to have all our members and our linkshell itself prepared by the time actual endgame content comes out. Until then it is just a matter of keeping everyone involved and getting a chance to all work together on the limited "endgame"-ish goals the game currently has to offer. It's all just practice at this point, but I'd still hate for someone in our LS to feel alienated from LS events. So for me at least that takes precedence over progression (especially since progression at this point is so limited, it is an easy choice).