Random note before I start my actual contribution: I have Darkrai carrying Life Orb because it gives us a guaranteed 2HKO on +1 Arceus-Ghost after SR. Leftovers eliminates that opportunity entirely. Considering our method of handling it is with a Dark Void followed with Dark Pulse spam or NP+Dark Pulse, the fewer turns we use are the better. Dread Plate is an option, but we only get 78.91% odds.
Now... what to do, what to do. Several threats that need to be addressed have been brought up, and if we want to avoid redundancy it's becoming clear that we're going to need to reassign a teamslot or two. Unfortunately, we've dug ourselves into a pretty deep hole, as solving one problem is inevitably going to lead us into redundancy. Replacing Dialga with SDef Jirachi seems like quite a good idea, although we will inevitably kill offensive momentum by using it unless we opt to do something ridiculous like run CM Jirachi in Ubers. (you asked for innovation, you've got it) Jirachi would help leaps and bounds against Scarfed dragons and Mewtwo, but it unfortunately opens us up to one of the specific things that Dialga actually blocked quite well, namely weather sweepers. Of course, we have a sixth slot, so we could run something like Giratina-O.
tl;dr: CM Jirachi (aka sir Walledbylots) over Dialga, Giratina-O of some sort in the last slot.