I do kind of have a problem with that. It's limits the freedom Mega Man was based on. You should be able to go wherever the hell you want, whenever the hell you want. Same goes for MM&B's branching path mess.
But what really got me about MM8 in particular, though, is that this split caused a break in the weakness circle. At least MM7 and MM&B had one concrete loop. Also, this caused Sword Man's stage to absolutely depend on the first four boss' weapons. I don't like that practice, either. It's fine for a Wily stage to demand you use a specific weapon to progress, but it's not cool for a Robot Master stage. It doesn't stop me from playing the game, or even enjoying it. It's just a pet peeve.
I didn't mind the 4-4 setup *IF* there is some design point to it, as there was in 8. The later-half use of weapons is something I actually liked. The fact that it's not fortress-exclusive, once in a while, makes the concept feel slightly less gimmicky. That's not to say I'd want every game to do it that way, just saying, it was a nice change of pace. Whereas most other Classic-series "change of pace" stunts tend to go pretty badly.
However, I do agree that the X4 setup is best. But I will also say, I am GLAD that so long as MM8 chose to split the bosses, that they also split the weapon cycle with it. To do otherwise is to create an obvious "preferred order" which only serves to limit MegaMan's trademark freedom even greater (one of my many gripes with X5; even though all 8 are accessible the actual game progression is centered on a 4-4 setup, with Grizzly to Red being the obvious preferred order).
MM8 was not the first game to break the weakness cycle, though. 3 did that, with Snake, Needle, and Gemini being off on their own. And I actually didn't mind. The fact that, even on a perfect replay, you have to pick more than one boss to tackle with the buster, kinda spruced things up a bit. Then again this was before we had intermission bosses.
Also on DeviantArt, Rumble, DLive.tv, and the Fediverse (@freespeechextremist.com and @bae.st)