Patraic i suggest giving Taunt to Mewtwo instead of Protect.
Weather he runs protect or Taunt mainly depends on who will be on the feild w/ Mewtwo. If it's Kyogre or Snolax, than it's better to keep Protect so Snorlax and Kyogre can Explode and Surf whenever they need to. Or, if he's sent out w/ Ogre, then you can run Taunt and just use Muddy Water. Keep in mind Muddy Water's accuracy, though....but Taunt can still be an option.
I have alot of options, but I don't know which ones to go with. Can anyone help or at least give me a pointer or two?
When you said "I have a lot of options", you hit the nail on the head. As I mentioned earlier in this thread, Mewtwo is an incredibly variant Pokemon, and will usually fit quiet well on any team bar TR. As such, it's kind of hard to say you will use Mewtwo, and base a team completely on that. You can base a team
around Mewtwo, but just saying Mewtwo will be on your team will not narrow down your options.
The only real constant on Mewtwo is Grass Knot. Everyone picks Grass Knot because it hits Kyogre and Groudon harder than Solarbeam and Thunder, especially since Grass Knot can be used in any weather and to hit both of them for SE. That, and a lot of people use Protect on Mewtwo to further broaden the number of Pokemon he can Partner w/, allowing to partner w/ a Pokemon like Meatgross, Zapdos, and Kyogre, who will eventually need to use an attack that hits everyone on the field, including their partner. This is especially true on Pokemon like Snorlax and Meta, who will have to Explode as soon as their HP starts to dwindle, because they usually won't be able to outrun the opposing Pokemon in time to blow before being KO'd.
When you say a backup for Palkia, you mean another sweeper who can come in after he is KO'd? If that's the case, then it depends on weather or not you will keep a rain dance team. If you plan on keeping a rain team, than Ludicolo or Zapdos might work. If not, than you have even more options, like Lati@s, Infernape, and Garchomp.
A Pokemon like Toxicroak can't really take any attacks too well, just like Shiftry and Ludicolo (although, Ludi does have good Sp Defense). Toxicroak's main niche is being able to take no damage from Kyogre's Surf, finish weakened Pokemon w/ Sucker Punch, take out Dailga, Abomasnow, and T-Tar w/ STAB Cross Chop or Low Kick, and lastly, to Fake Out and give his partner a chance to do what it needs to do.
If you have Grass Knot on Mewtwo, and not make Kyogre your lead, then you might not need to make Kyogre slow. You can have your 2 leads able to function w/ or w/o rain up, take out opposing weather inducers, then switch Kyogre in to get a guaranteed rain later on in the battle, no matter what your speed.
BTW, I wouldn't recommend testing VGC teams on PBR random wi-fi battles. A lot of the teams focus on different rules than VGC on PBR, and over half the stuff on random battles will never be encountered in VGC (like Roar of Time Dialga) because a lot of those teams are being tested out for different tiers, different tournaments, etc.
