Whew, I'm finally done...
Here, I fixed everything but Suicune
Magmar's ribbon thing is an error, so it having the Classic Ribbon is all right. However, that event was exclusive to X and its origin game appears as Y, so I corrected that.
And about the rest...
Mewtwo: PID type was "None" and had nature mismatch.
Latias: Same as Mewtwo.
Latios: Same as Mewtwo.
Kyogre: Same as Mewtwo.
Rayquaza: Same as Mewtwo.
Uxie: Same as Mewtwo.
Ho-Oh: PID type was "None". No nature mismatch, but still a problem.
Togekiss: Same as Ho-Oh.
Dialga: Same as Ho-Oh.
Giratina: Same as Ho-Oh.
Arceus: PID-Nature mismatch. The thing's proper nature was Calm.
Meloetta: As Sirnight said, its only issue was its SID not being the correct one. Where did you get this thing, anyway?
There are some things for me to clarify, though:
As I previously stated, can't help you with the Suicune. The reason for this is that I'm not sure about what PID type do gen 3 roamers use.
Fixed everything else. Most of them required PID Method 1.
The only exceptions to this are:
>Arceus: Fixed it with Method J in order to keep the Modest nature, and, according to PKHeX, it was the correct one, but I cannot confirm that by any other means, so do be careful with it. [Edit] If you'd simply rather having the nature fixed, take this one instead
>Togekiss: Its PID type had to be Colo/XD. Also, changed its ability to Serene Grace 'cause no one likes Hustle. No one.
Made all of them as competitively useful as possible nature, IVs and ability-wise while remaining legal (though, if you aren't satisfied with some of the IVs, Hyper Training is an option). Don't even know if you're actually into competitive battling but I thought if I was gonna help I might as well do that part of the job. That's why I took so long (found this topic a couple of hours ago).
Made the shiny ones keep their shininess without changing the TID/SID combination, but their IVs aren't all that good as a result so you might find Hyper Training more necessary for them. Made'em hold Gold Bottle Caps just in case (even though you can inject them into your bag anyway xD )