Bosses have always been memorable, but I don't think there was ever a heavy focus on them until perhaps Fusion. And either way, combat encapsulates far more than just bosses, Mark talks about the moment to moment gameplay being particularly combat heavy, which is not Metroid-like at all and one of the things that concerned me as soon as I learned of the melee counter.
Have you ever played Super Metroid? Every boss battle in the game is a stone cold classic, and you won't find many write-ups or retrospectives on the game that fail to mention them at length.
And Metroid 2 literally has a counter of how many bosses remain in the corner of the screen at all times. I spent hours as a kid looking at the pages in the instruction book that had pictures of the various types of Metroid on them. (It was the nineties. It was boring sometimes.)
I don't dispute that the moment to moment combat between bosses in the 2D games has always been a fast-paced, almost incidental affair, but the series is not comparable to something as bloodless as Mirror's Edge, where combat was something to be avoided.