In D/P Deoxys can be in any form you want, and since Arceus is in the running, we're talking in terms of D/P, meaning Deoxys-A is accessible. Don't judge something based on the title it's given. Goldeen is called the Sea Queen but we all know damn well Goldeen sucks. And if you meant "best," then you should have said "best." The definitively "strongest" Pokemon is Deoxys-A.
Ok, I made a mistake, but my English isn't perfect 'cause I'm Portuguese, I didn't remember the word "best".
Deoxys is sure a strong Pokémon, and I admire it, I think It's great, but for me this is the order of what I think:
1 - Arceus
2 - Deoxys
3 - Rayquaza
4 - Mewtwo
5 - Lugia
Why? Some of you ask this question. i'll tell the reasons.
1 - Arceus can have any type you want, can learn a lot of moves, has super-high base stats, and is called "the God of Pokémon", which means it is the... I'll call it "supreme ruler".
2 - Deoxys is a strong Pokémon too. Has many forms, but in every form he has high base stats, specially Attack and Speed. Even in Defense form Deoxys has higher Attack Stat than many Pokémon. Is a Psychic Type (one of the best) and can learn many powerful attacks.
3 - Rayquaza is a super-speedy Pokémon with high Attack too, is a Dragon Type, can learn many attacks too. When in levels 50+, he has super high Speed.
4 - Mewtwo is very strong in Attack and Speed, but you all have forgotten one thing: Defense. Mewtwo is one of the worst Legendaries in terms of Defense. Even Togetic, a weak Pokémon, and Chansey, weak too, have more Defense than Mewtwo. So, for me, Mewtwo isn't in Top3. Cannot learn so many attacks like the Top3.
5 - Lugia. The best Legendary Pokémon in terms of Defense (Not counting Defense form of Deoxys) and strong in Speed. Can learn Water, Fire, Electric (few), Dragon... Many types of attacks. Great Pokémon too.
These are my reasons. If you have anything against them,you're free to post. You're free to have your opinion.