I liked the way it's related in this game.
Seeing how those stars are linked by Destiny, even in acting in completely different ways, was a nice point of view for me.
First of all, I agree with EstrangedIX. Leknaat didn't want to be involved in this affair for affective reasons.
Then, I don't think she was necessary to the plot, neither the 108 stars actually.
The Tenkai star is not the hero, he's just de HQ master and he doesn't have a True Rune.
Main characters - Hugo, Chris, Geddoe and Luc (we can even add Sasarai) - don't need to be guided or oriented. I mean, Geddoe already know the story and when Hugo and Chris get their True Runes, they also know the role they have to play from now.
Then about the stars to recruit, most of them are not recruited to fight but they're sent to the Budehuc Castle to be in a neutral land and live in relative peace for this time of war. Then they really act as "stars" when the HQ becomes a place for refugees.
After all, the army is not really build by optionnal characters but more by automatic recruits.
I'm not saying I wasn't surprised by the absence of Leknaat and the minor interest of the Stars of Destiny. But when I think about it, I really think she wasn't needed in this game.
You're saying the game was missing the "glue" that held the previous games together. Well I'd say the opposite. This game really gave to Suikoden world a lot of depth (geographically and historically), more than those usually enigmatic Leknaat's appearances
To end this, I also agree with you on one point. The story focus a lot on Luc.
Personnaly, I see Suikoden I, II and III as a trilogy centered on Luc (we have known him young and adult, and we know what he lived until his tragic end), that's probably why I'm considering Suikoden III as a good conclusion and why I'm not expecting a sequel (even if I'd like to know more about Viki, Jeane, Leknaat, Pesmerga, and a lot more characters...).