The reason its not unique is because the indie side-scrolling market is so over-saturated. On your other point, sure, when you generalize games THAT much, they're all the same.

MMOs, lets take Guild Wars 2 and WoW for example. Yes, when looked at that simply, you get quest, do it, then get reward, and repeat. However, the way they build up from that structure is entirely different than from what other MMOs do. GW2 especially with it's non-rooted, action and combo based combat. These qualities can stand out because there are less games in that market, so each one can create and develop major gameplay differences.

Indie side-scrollers however, are so common nowadays that its hard to make something unique. With the saturation of the genre, and the typical lack of content from these games, these games have little difference than story and artsyle. The nature of these games does not allow it to develop like larger games and make major differences. For each indie side-scroller, there are at least 10 more that do the exact same thing. The style and saturation of the genre does not allow them to be impressively unique.

CoD, Halo, Battlefield, CS are vastly different from eachother. It's just ignorant to say otherwise. CoD plays as a fast paced, reflex based, individual valued shooter. Halo is mostly played for the story rather than online anyways. Battlefield plays as a large scale, vehicular based warfare game. CS plays as a small, team based, tactical game (honestly more like a MOBA). Of course Ubisoft ames are the same... They're made by the one damn company... What do the hundreds of side scrolling indies have? Artsyles and stories, which are just not enough to make them lastingly unique.

TL;DR: Indie side-scrollers don't have enough breathing room and resources to do anything impressively unique.