I'm seriously doubting your choice of deoxys lead, generally deoxys-a is superior for a mixed attacker/hazard layer, but you can only rely on it for SR. Normal deoxys form is pretty much just as frail, and doesn't hit as hard. If it works for you, however....
Wobuffet cannot effectively run destiny bond without custap berry. End of story.
Change your scizor build to the specially defensive uber edition, it NEEDS that sp.def to absorb power dragon attacks that run rampant in the metagame. Also, although I believe that good ubers teams should have at least one steel I feel it should take on a more defensive role, rather than a scouting role, as that role is currently usurped by scarf-zekrom to an extent which is SO much stronger, faster and bulkier, and scouts with volt change, and can even clean lategame with its incredibly powerful stab moves. You may want to consider a scarfkrom.
I really feel that in the V gen meta manaphy is not effective anymore, it isn't fast enough and there are less situational and more powerful sweepers. Psycho Break mewtwo for example, or even nitro charge reshiram, although that goes against your rain team. You may consider trying a bulky water arceus set, with calm mind, judgment and significant defensive EVs.
This still leaves you extremekiller arceus weak, and to be honest, there are few and far counters inbetween for that. The best counter is probably a defensive groudon with roar /dragon tail (but even that is severely wounded by sun boosted overheat), likewise with skarmory, and those two do not fit your team well. Normal arceus not carrying shadow force however, are manhandled by ghost arceus (although I did suggest water arceus), so perhaps a giratina would be more apt, it can burn arceus and phaze it out, also spinblocking hazards, which brings me to my next suggestion.
A nattorei as a defensive steel pivot, your team greatly needs an electric resistance / immunity, and whilst sp.def nattorei is greatly hurt by CB lightning strikes, it's far better than taking repeated volt changes to the face then getting swept lategame.
A more controversial suggestion to fix your zekrom weakness, a dugtrio, but that is highly situational and needs a team built around it. So I cannot wholeheartedly suggest it.
Currently --> Huge weaknesses to zekrom / extremekiller arceus / CMMewtwo (only possible check is your scizor if he doesn't have flamethrower (and then aura sphere still hurts) or a healthy wobby.
Zekrom checks --> Arceus ground / Steelix (lol) / Nattorei / Dugtrio (only choiced ones, any non-electric attack rapes duggy).
ES Arceus checks --> Skarm/Groud (without overheat) / Ghost arceus / Giratina (without shadow force)
CM Mewtwo checks --> Tyranitar (non-aurasphere versions) / Scarfrai, Scarfmin (shaky, with two many CMs you lose) / Specially defensive scizor (non-flamethrower versions)
DD/SD Rayquaza --> this one just popped into my head, and reminded me you have a general problem with setup sweepers due to your lack of scarfers, basically, if you misplay wobuffet or it is severely weakened you're going to have a problem. Even with stuff like RP groudon / paradancer groudon (no electric immunes = a fully paralyzed team).