hmmm i remember the fillers a little differently than you... in my opinion about ~70% were like

"we have to go help/kill XXXX he might have a connection to orochimaru" <--- and most filler characters had some special powers given from orochimaru

so i think the filler characters in shippudden have some connection to the story too.. maybe some agents from akatsuki or so... who knows what they were searching in that ruin there.