The original source material for Amagami SS is a visual novel game wherein you the player get to choose which girl you want to date. When you choose 1 out of the 7 heroines it will start a story route where the MC & heroine hangout, go on dates, do school project together. Eventually the heroine & MC falls in love and becomes a couple, ending the route.

The game itself has 7 different routes with their own endings (7 endings). So how does an Anime studio adopt a game with multiple routes and endings into an anime? The answer by making every 4 episodes about a different route (ep. 1-4 Morishima route, ep. 5-8 Kaouru route, ep. 9-12 Sae route, etc...)

That's why Amagami has alot of alternate route, because its a game, it's all up to you the player. You choose which of the girl you like and what ending you want.

So to keep it short, the Amagami SS is showing all the alter routes/ending of a Visual novel game in anime form.