Yeah the huge materia stuff really is a big plot hole. I mean at least Shinra are actually using it. You steal it from them and... what? It just sits in Bugenhagen's observatory. You can't even get anything out of them until you've done a crazy amount of work. You can't get Master Summon until you have all the summons but if you have Knights of the Round then you sure as hell don't need Master Summon to beat Sephiroth.