Well, the reason for several of these characters vanishing goes back to Clannad's origin.  At first, it was a visual novel with multiple endings, a different story path depending on who Tomoya ends up with.  As I understand it, the other characters don't really have as much reason to appear in those routes one you're locked in (I haven't played the game, but it seems logical).

If I recall correctly, Nagisa is the only heroine with an "After Story" arc--everyone else's arcs end with them still in high school.  The anime adapts several of the routes as smaller story arcs (as is usual with these sorts of adaptations), and the Tomoyo episode is based on Tomoyo's ending, but once you get to a certain point, I believe it's all based on Nagisa's After Story route.  Beyond that point, they don't really see much reason to bring the other characters in much at all, with a few exceptions (and another alternate reality episode like the Tomoyo episode).

It's definitely disappointing when you get to care about those other characters, but it does make sense.  This also plays into the issues with the final epsiode, but I'll save that rant.

WHERE IS THE DANGO SONG?!  IS IT WITH SAMANTHA?!

Anyway, hoo boy the last episode sounds fuuuuuuun (sarcasm).

I can see why it would be unliked if that's how it ends, but I'll try my best to forget the hours my soul has spent crying in a corner long enough to try and watch it as it's own thing.  (I just got to the part with the engagement, but I'll talk more on that later).

I guess that does make sense, but I guess I think it's just a bit of a waste, you know?  So many interesting characters, and they all kinda sachet off...

They probably thought the Dango Song was too happy for the series they were planning out.

Actually, you shouldn't take the last episode as its own thing--the only chance of making sense of it is in tying it back in with things that have been going on in the rest of the series.  But, again, you'll get to that.

Yeah, I know what you mean.  We needed much more Kotomi.  I guess the writers figured that the viewers can always play the visual novel to get more of the other characters, but that doesn't exactly help those of us who live in a region where said game has not been released...