I believe the difference between ferrothorn and deoxys to be this: if a ferrothorn comes in and you switch out to something that you know will ko it, such as volcarona or infernape, it sets up sr, you kill it, and are in a pretty favorable position. Now, when dealing with deoxys, you have Pokemon that can outspeed it, and Pokemon that can ko it, but few that can do both. Even things that do both, such as genesect, have a hard time with it. Killing deoxys with a CB tyranitar puts you at quite a momentum disadvantage with a HO team, such as an opposing lucario about to sd up, whereas with ferrothorn most things that can kill it retain enough momentum for a team. Deoxys not only garuntees SR up in a match, but forces you to also kill it that turn to prevent spikes up. That's the reason azelf exploded once it put up SR, to generate momentum for a team. If you DON'T kill that deoxys immediately, then it's got even more hazards up, but deoxys forces you to kill it right then and gives its team an indirect explosion in the process. You know you have to take it out as soon as possible, and that can be capitalized on.
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