Sitting back and waiting and letting the mortals do whatever they want with magic didn't work too well with the whole Well of Eternity thing, from Malygos' perspective, as most of his dragonflight got wiped off the face of Azeroth during the war that followed. Sure, Neltharion/Deathwing's to blame, but would he have ever been able to convince Malygos that the Dragon Soul was a good idea without the Burning Legion breathing down their collective necks? And despite the repeated danger of demonic invasion, the mortals just keep using magic, summoning demons, blowing up fonts of mystical power, and generally getting way way out of hand. From Outland to the Sunwell to Nordrassil, there's plenty of examples of reckless mortals getting ahead of themselves with magic. So it's not terribly surprising that a restored Malygos would want to get more hands on and keep this all in check.
The problem wasn't that Malygos wanted to control magic, but how he went about it. First off, Alexstrasza of the Red Dragonflight personally owed the Kirin'Tor and its leader Rhonin pretty big for their role in destroying Deathwing's Demon Soul and returning its stolen power to the four aspects who'd been duped into creating it (as the Dragon Soul) so long ago. Even Malygos was in their debt. But even that might not have been an issue... after all, even the Kirin'Tor had to recognize Malygos as the Aspect of Magic... if he hadn't decided to go ahead and just move ley lines around without regards to the earthquakes and other disasters he was causing in the process. Enormous tears in the land and undersea rock formations began to form as Malygos directed the blues to divert magic from its long established courses and collect it in places held by his dragonflight. Worse, in a sign of his own growing hubris, Malygos not only refused to discuss his actions with the other aspects, but he actually used the stolen magical power to attack them at the Wyrmrest Temple in the Dragonblight.
It was bad enough that the Scourge under the Lich King were digging up dragon skeletons and turning them into undead wyrms to serve in his undying army, but now Malygos prevented any sort of unified effort to deal with this threat by turning his blues loose to attack and harass the formerly inviolate neutral ground and meeting place of all the dragonflights. In the end, even the life loving Red Dragonqueen herself could no longer endure her brother's casual disregard for the cost of his actions and his heavy handed dictatorial approach to his charge. When adventurers presented her consort Krasus with the key to the focusing iris carried by Sapphiron in undeath, she sanctioned an assault on the Eye of Eternity itself, Malygos' lair.
In the end, despite all his vaunted mastery of magic, Malygos fell before a combined force of mortals and red dragons. His death (the first time an Aspect has actually died) leaves many unanswered questions. While magic existed before the Aspects and will continue on (as it does on worlds without Aspects, like Outland) there is now no appointed guardian for the ebb and flow of its day to day use. Is there to be a replacement? While Nozdormu the Aspect of Time has long known his exact moment of death, the blues did not share his foresight and it is at present unknown if there is even a mechanism short of a Titan's will to replace a fallen Aspect. While Kalecgos seems to have returned to serve as Ambassador from the Blue Flight to Wyrmrest Temple following Malygos' death, it's not currently known who, if anyone, leads the blues.
Post Nexus War, the blue dragonflight is at once bereft (this time permanently) of their 'father' and yet in possibly the strongest position they've been in for centuries. They've shown they can actually wage war against the combined forces of the other four dragonflights and deal significant damage, and their numbers are as high as they've been since the Sundering. It's yet to be seen what role the blues might play in the future, but their past is one of strife and loss, and their charge remains to control the reckless magics of Azeroth.