same here; the anime ending gave it a bit more of a unique charm from average harems. besides, there were too many loose ends in the manga. for example, we don't know how he met the three due to his amnesia (although, i'm not sure if the anime is supposed to fill us in on us; i thought it was usually the manga that filled in the missing pieces for the anime, not the other way around).
but yes, the manga ending was sweet but (for myself) unsatisfying.