Da Capo Filler Guide:

The original Da Capo game was more of a prototype than a completed project.  Clearly, the designers of the game had a cool idea about an island full of cherry trees that granted all wishes, good and bad.  But in the original game, only Sakura's bad wishes were granted, whereas for everyone else only good wishes were granted.  This unfairly made Sakura out to be the villain.  In Da Capo II Sakura is the hero who protects the island from bad wishes.  It's exactly like the difference between Terminator 1 and Terminator 2.  T2 was just so much better.

The visual novel tried out a lot of ideas, most of which were awful and boring.  But the story that stuck was the story of Nemu and Sakura.  It is the 'true' route that the rest of the series follows as actually having happened.  The anime was wise to adapt this portion of the visual novel, since the rest was no good anyway.  Strangely enough, though, even the Nemu and Sakura routes weren't transcribed very well from visual novel to anime.  A lot of portions of both routes are just left out, missing, never to be seen.  In place of these important elements where we get to know Nemu and Sakura, the anime gives us a bunch of useless filler.  Even with 26 episodes, covering just two routes, they manage to not deliver a finished product.  Whatever animation studio did Da Capo has to take a lot of responsibility.  Not only is the story in shambles, but the resolution and art quality is dirt poor.

Still, the series tried its best to cover the non-romantic portions of the stories that involve Kotori, Miharu, Yoriko and Mako.  Leaving Moe out entirely was probably a good idea because her story sucked in the visual novel and no one would have wanted to watch it as an anime either.  It's also important to watch the Da Capo anime so people will understand what's going on when watching the wonderful sequels to Da Capo -- Da Capo Second Season (D.C. S.S.), Da Capo II  (D.C. II), Da Capo II Second Season (D.C. II S.S.), and Da Capo III (D.C. III).  Without the original romance between Jun'ichi and Nemu, none of the events in the following series would have ever occurred.  Yume and Otome are Nemu's granddaughters, Nanaka is Kotori's granddaughter, Miharu is Minatsu's prototype, and Yoshiyuki is Sakura's son.

To make for the most pleasant viewing of Da Capo possible, here's a guide on how to avoid as much filler as possible:

1.  Skip all the side stories!  They're worthless and all of them have nothing to do with the visual novel, they were just made up for no reason to waste our time.  These stories lurk around the endings of most episodes but also sometimes appear at the beginning.  You can tell it's a side story when the scene makes no sense and is completely unrelated to the actual series events that happened right before it.

2.  Skip episodes 6, 8, 9, 13, and 15.  They didn't happen or they're recaps so they're a waste of time.

As an interesting side note, the Suika visual novel is also available in English and is a prequel to Da Capo.  Sayaka Shirakawa is actually Kotori Shirakawa's cousin and even shows up in the Da Capo visual novel.  Throughout the Da Capo anime they make references back to Suika, which is a sort of fun easter egg hunt.  So if you just can't get enough Da Capo, go ahead and read Suika as well.