Yeh that certainly is part of the problem, which is why I emphasize the anime as I have not played the VN. The article I linked also mentions that as a major issue. The anime studio should've realized that trying to cram in multiple routes just won't work well. But then again there are all the fan expectations of having their favorite girl featured. That said, that's not a valid excuse. If you want to make a proper anime adaption then do what's right.
Well, enough of me bashing Clannad.
Though, talking about adapting visual novels actually reminded me of Steins;gate. I actually really like that anime for the most part but it also suffers from some weird plot points and pacing, which come from their attempt to give every character their own episode at some point.
Adapting Visual Novels in really problematic because:
A) You've got to deal with the extremely text heavy, book like nature of the original works which weren't created with animation in mind and
B) The problem of dealing with multiple story paths.
By itself, A) shouldn't really be that much of a problem because a really talented director would find a way to convey the text through visuals, or cut the text down to it's essentials, or some combination of the two. However, most of the time, it seems that directors/writers just try and stuff all the words of the VN into the anime leaving making the show bloated and poorly placed. The same seems true with wordy LN adaptations.
B) Could be fixed by simply deciding on a canon route but studios are creating these shows to appeal to the fans and so they end up pandering to as many people as possible.