This is a quite common question among X-MEN lovers. A lot of documents arguing this matter are found.
Who are the most powerful, Strongest and Weakest X-Men
The Top 25 X-Men
The Top Twenty X-Men of All Time
The Top 10 Most Powerful X-men
Now, I will explain who is the best mutant. But unfortunately, I have not read X-MEN comics. Therefore, my hypothesis is derived from only the movie series, X-MEN, X2, X-MEN the last stand, X-MEN the first class, and 2 films of Wolverine series.
First of all, telepathy is the strongest ability of all supernatural powers, as I mentioned before. No matter how physically strong, he will be defeated with his mind out of control.
Besides telepathists, Magneto and Deadpool are the top 2 mutants, I think. Magneto has absolute power of modifying metal. He can manipulate Golden Gate bridge. However, attacked by the telepathy of Emma Frost, Magneto had to escape from the battle. Deadpool has enormous abilities such as teleport, blast beam, healing and so on. But I guess he does not have a strong mind to be resistant against telepathic attack, although there is no such a scene described in the film.
Then, there are lots of telepathists in the films.
1) Professor X
2) Jean Grey and Dark Phoenix
3) Emma Frost
4) Jason Stryker
5) Kayla (Silverfox)
So, who is the most powerful?
The ability of Professor X is extremely dreadful. If he wants to, perhaps he can kill all human in the world using Cerebro, a machine to reinforce his telepathic magnitude. However, he had been controlled by Jason in "X2."
Jason's telepathy overcame Professor. But Jason could not control himself. I think nobody would accept that he is the most powerful mutant.
Jean Grey has telekinesis, in addition to telepathy. She reincarnated to Dark Phoenix in "X-MEN the last stand." Dark Phoenix can disintegrate anything she hopes so at a glance. It is incredible! She would be the champion. But, she also could not manage herself. Uncontrollable power is no more power.
How about Kayla? She could controlled Wolveline, but could not defeat Sabertooth even if she delivered her power directly. The magnitude of her telepathy seems not to be strong enough to match Professor.
The last one is Emma Frost. She is a smart telepath. I guess that her power is not so strong, hypothesizing from the fact that there is no scene that she annihilate other people with her telepathy. But she has another ability. She can change her own body to crystal. It enhances her physical toughness. In addition, her crystallized body is immune to telepathic ability of enemies!
That is, Emma can perform both attack and defense at the same time. This is unique to her. Therefore, Professor and Magneto had to cooperate with each other to capture her. If Professor had fought with her, he would have lost.
In conclusion, the most powerful mutant is Emma Frost. This is a little odd, but logical opinion of mine.
My past entries as references:
What is the strongest supernatural power?
X-Men and psychiatry (3)