Wobbuffet vs Suicune

You cannot switch out wobbuffet because once you do it's effect will stop scince it's an ability. The only way to switch without letting it escape would be if you switch it with another Pokemon who has the same ability as wobbuffet. If you don't have another Pokemon with that ability then you will have to attack with wobbuffet. Scince wobbuffet is a defence type Pokemon you will have to teach it a attack if yours doesnt already know one and try to catch it. It's going to be a little tough but if you try you should be able to get it.

If you switch Wobbuffet then Shadow Tag won't have any effect anymore. Wobbuffet can learn attack moves, even though it is a defensive Pokemon. So teach it an attacking move and damage Suicine.

It doesn't matter if you don't have a Master Ball - well it does, you need it for Mewtwo. But you can catch Suicine with an ultra ball, just have some patience.

Once you call him back the ability will end, try using Golbat's eye trick, it prevents the target to leave and you can call him back. Just be sure to get him back out before the eye thing quits.

First you shouldn't have used your masterball you can catch Mewtwo with a pokeball...

I wasn't able to catch Suicune without using a masterball

Mewtwo and Suicune are both possibly to catch w/o the Master Ball as I learned ( I used my master ball on mewtwo beacuse I didn't have a sableeye or timer balls) but it will be very hard, just be careful not to kill it oh and btw, the only way to get suicune on firered is if you actually picked Charmander, if you picked Squirtle you can get raiku and Bulbasaur will get you Entei. I hope this helps