The mutant island nation of Krakoa has fostered in a new era of independence for the X-Men and has ushered in a new golden era of prosperity for mutant kind. The X-Men's first island, however, was only a temporary headquarters, originally owned by their former nemesis, Magneto.
Island M first appeared in 1964's X-Men #4, by Stan Lee and Jack Kirby. This mysterious island was raised from the bottom of the Bermuda Triangle by Magneto, and was used as a headquarters for the Brotherhood of Evil Mutants. Magneto clashed with the X-Men several times on Island M, along with other heroes like the Avengers. Island M was seemingly destroyed in the pages of 1968's Avengers #53, by Roy Thomas and John Buscema.
Even so, Magneto eventually returned to Island M, restoring it just in time for a major battle between him and the X-Men that took place in 1981's Uncanny X-Men #150, by Chris Claremont and Dave Cockrum. This time, Magneto threatened the world's nations, telling them to disarm their nuclear weapons or be destroyed. After the X-Men defeated Magneto, he fled, and Marvel's Mutants claimed Island M for themselves.
When the X-Mansion was severely damaged in issue #152, the X-Men took advantage of their newly claimed island. Island M became a temporary headquarters, valued for its advanced computer systems and technology, where the X-Men hosted guests such as Carol Danvers and the Starjammers.
Initially, Island M was a fairly nice headquarters, much like Krakoa. On a deserted island, the X-Men could relax, without worrying about persecution by humans or an attack by one of their many enemies. In this way, Island M was similar to Krakoa, which also acts as a safe haven for mutants. While it's true that the X-Men didn't stay on Island M for very long, it was technically their first island base.
One of the major problems with Island M, however, was how creepy and mysterious it could be. 1987's Marvel Fanfare #33, by Chris Claremont and June Brigman, revealed that Island M was originally inhabited by malevolent creatures called the Ancients, who left a disturbing mark on the island's citadel. This dark history led the X-Men into conflict with the Chief Examiner, who released some of the Ancients' evil forces.
Although Krakoa is not home to inherently evil spirits (other than the former villains living on the island), 2019's Powers of X #4, by Jonathan Hickman and R.B. Silva, revealed how Krakoa was tragically split from its counterpart, Arakko, long before human civilization. In 2020's X of Swords: Creation #1, by Jonathan Hickman, Tini Howard and Pepe Larraz, this history initiated a conflict between Krakoa and Arakko's forces in Otherworld.
While Island M was originally the headquarters of Magneto, Krakoa was also originally an enemy of the X-Men, capturing the original team back in 1975's Giant-Size X-Men #1, by Len Wein and Dave Cockrum. Despite their initial similarities, it seems that Island M became more dangerous for mutants than Krakoa. For example, in 1982's Uncanny X-Men #160, by Chris Claremont and Brent Anderson, Belasco and his horde of demons attacked Island M and abducted Illyana Rasputin, subjecting her to years of torment in Limbo.
Krakoa, on the other hand, has proven thus far to be much safer for mutants. While the island was attacked in 2019's X-Force #1, by Benjamin Percy and Joshua Cassara, the mutants on the island later formed X-Force as a countermeasure against such an attack happening again. As a whole, Krakoa is much more stable than Island M, acting as a true nation rather than just another headquarters.
Island M had its perks, such as a training arena for the X-Men. Even so, Krakoa has the Quarry, which is also built for sparring sessions. Moreover, Krakoa is a home for all mutants, with a plethora of features, including gateways that travel all over the world. One of these gateways also travel to Island M, which became a Krakoan habitat in 2019's Powers of X #5, by Hickman and Silva. Island M's place within Krakoa demonstrates how all-encompassing Krakoa is compared to Island M. Regardless, Island M was still a good start for the X-Men's path towards Krakoa.