I played through and beat both of them on 3DS. I preferred Mighty Gunvolt Burst. It was more focused, but also more linear. If you want more exploration, then go with Blaster Master Zero. But for a straight up, solid, streamlined action game (with enough variety and experimentation of its own) then Gunvolt is your boy.
I prefer Blaster Master Zero. Partly because I prefer the exploration, but also because I didn't feel that Mighty Gunvolt Burst handled its features in the best way at times. The countless ways to customize your weapons are awesome, but the system feels too deep for the gameplay system they're featured in to me, if that makes any sense. They're both good games though, and I don't think you can go wrong with either one. Go with whichever one you think is closer to your preferred type of gameplay.
If you've played the original Blaster Master, you can skip Blaster Master Zero IMO. It doesn't have as many bells and whistles added onto it as I thought it would, though it definitely has some. On the other hand, if you haven't played Blaster Master and would like to, BM0 is probably the best way to experience this unique cult classic.
I haven't played Mighty Gunvolt Burst but plan to eventually. It looks like a solid enough Mega Man-esque game, and I expect it to be more enjoyable than BM0 was (for me personally).