Objectively, no difference if your water in both methods is from the same source. Heat is heat. Your water might pick up some particles from the container it's in affecting the flavor in some small way.

Subjectively as a US tea drinker -

I find that filtered water makes terrible tea. It ends up flavorless. Spring waters and mineral water tend to make better tea to me. It's like the tea needs some sort of metallic content in the water to coalesce around to create flavor.

Water boiled in the microwave seems to cool off faster than water boiled on the stovetop or in a kettle. I've never measured it though. I drink it both ways but I tend to prefer tea made with water from the kettle. Maybe the metal kettle imparts some of its metal to the water. Maybe the water is hotter when it hits the tea than water from a plastic measuring cup in the microwave. Good tea should be "surprised" by the water so you should always pour water over tea rather than the put tea into water. I wonder how much of the subjective opinion of water preference has to do with which method people use? Perhaps when they use the microwave they are microwaving the water in the mug and then adding the tea to it rather than the other way around as they do when using a kettle. This does make a discernible difference in taste for good quality tea.