You're the only one thinking in such black and whites as "everything" preplanned or improvised.
As I have emphasized more than enough in this thread, gaming is a format that lacks certain luxuries, they can not plan it all ahead of time. But regardless of that, there are always ideas of what they want to do and where they want to go floating about. How much is written down and how much is just in the mind's of the writer is unknown and largely irrelevant. Just as much, the relative amount of preplanning or improvisation is irrelevant also.
Kitabayashi had an idea, he proposed it and they agreed as a team to work on it. If any on the team cared about continuity with the Wily storyline, it would have been taken into account when the setting was being made, plain and simple. If they cared or if nobody cared, you can only conclusive note that they did or didn't once the end of the storyline is reached.
If it's completely preplanned, the Wily X7+ connection wholly depends on what that plan is. If it's completely improvised, all the better as they can just decide to make the connection whenever they please. The truth is in the middle, not in either of these black and whites.
Oh, I'm not thinking in black and whites. You just seem so certain that they have something in mind, and I was merely inquiring as to why that was.
I more than fully realize storytelling over the span of many games isn't easy, especially when it's handed off to several different people over the course of development. It is exactly for this reason that predetermined paths through the over-arcing storyline can simply not be done on a regular basis. There are some exceptions, yes, but it is certainly not the norm. This is also a reason why most developers only think one game ahead at most and don't go beyond that. Even then, there's no guarantee any pre-planning is done at all.
I just think you guys are looking too deeply into something that you really shouldn't. There is a plot to Rockman games, yes, but they aren't the main focal point, and I really doubt they ever will be. Most of the stories can be diluted down to "several big enemies are causing trouble, go kick their asses", along with a cliffhanger thrown in at the end to make the player want more answers (hence, want to buy the sequel that may come out). To argue over them is folly in itself.
Of course, my post will most likely be completely taken out of context in an effort to continue arguing for the sake of arguing, isn't it?