Leaving the audience to make inferrences on their own is not, in and of itself, bad story-telling. There isn't a need for lots of exposition and having a lot is actually detrimental. If you weren't going in like a child with ADD, almost all of the things I mentioned were very easy to deduce.
Vaan hasn't forgotten his brother by Jahara and Penelo certainly hasn't "forgotten herself". An absence of direct referrences to Reks should not be read like that. Reks was important for helping establish Vaan's character and his relationship with Basch; he was not there for Vaan to endlessly angst over as though he were Squall. Vaan is not solely defined by Reks. And not only is it impertinent to the development of the actual story to bring him up, but from the fact Vaan is no longer ostensibly angry about Reks' death, we can infer he was made peace with it and it reflects a grown trust in Basch.
As for Penelo, I guess if you just sleep through every time Larsa joins the party, any subsequent interactions between those two characters, and the things she says in later areas (specifically Archades, because how she and Vaan feel about the Empire is important to their characters) I suppose you could make the case she was forgotten.
With respect to Ashe in the ending...did you consider her role as Queen would affect her ability to see her friends, and that (SPOILER)the way Penelo talks about her missing Basch suggests contact can't have been that badly broken? You can't notice that stuff from afar nor in a passing conversation.