I wouldn't make statements concerning Kyogre lightly, unless you've played a lot of Ubers. Having Kyogre on both Uber teams (lets face it, its usage is higher than even Garchomps in OU during DPP), does not make it balanced. Good luck finding a Kyogre counter that can't be beaten by one of its common sets. (closest you'll come without specialising is probably a 112 SpD Latias, which is still slightly specialized since the 112 spare EVs generally should do into HP). Simply, Kyogre arguement doesn't apply here, you're point is moot.
Similarly, good luck finding a way giving something +6 will stop you losing. If I give my Lucario +6, he'll pretty much ES anything that doesn't resist it, and I'm willing to bet with some entry hazards, anything faster less bulky than heatran which resists it will be OHKoed. Sure, you have a ScarfTar to stop me, but you have to wait 2 turns to revive it because I already killed it, during which time, I can dent the rest of your team. That being said, good luck beating my +6 Rampardos with your Scizor dead. Stockpile Hippo would be a nightmare to kill at +6 SpD, until you can revive something with Toxic (if you have it) and worse still, you'll only need the +3 since Stockpile helps you anyway.
Regardless of how abusable I think this Miracle Shooter is, the fact remains the only way to determine if it is broken or not is to test it. If you think of it, its basically the Ho-oh in OU argument. Its potentially broken, but we'll never know unless we test it. Similarly, Ho-oh would have no shot of being in OU if SR didn't exist, so arguably, an X-item clause could keep Miracle Shooter from being broken. Realistically, other than +6 (except maybe the +3), the next best effect is max revive, but granted that games will most likely into Revive Chicken (i.e. if I revive something, you'll just revive your check), it doesn't seem too broken.