"He pushed them aside by killing development systems (VB6,FoxPro)"
Except VB6 and Foxpro were never really developer tools. They were tools for non-developers to get basic programming tasks done. That was kind of exactly why they were developed- things like Visual C++ were always the tools targeted at professional developers.
"the Win32 API, to slowly become more irrelevant with endless layers of cruft built on top"
Win32 API became irrelevant, because it's become increasingly irrelevant. Why on earth would you want to keep an outdated API that's now decades old in it's design and origins as your primary development target when no one is using it? That just doesn't make any sense whatsoever. It doesn't make sense to maintain something that's inefficient to develop with, and I say this as someone who cut my teeth on Windows development with C and Win32 API many years ago. I have fond memories of it but I've no idea why you'd give a shit about it in this day and age.
Your argument is classic of someone incapable of dealing with change, which, in the world of technology is probably one of the least desirable traits you can have. You can boil your argument down even further when you talk about layers of cruft, you can say using C with the Win32 API is in itself a layer of cruft built on top of just doing everything in pure assembly, which is a layer of cruft on top of just doing everything directly with machine code and fuck the APIs.
"Ballmer wasn't bad; his jumping around on stage shouting "Developers!" showed that he knew what the true value of Windows was: the external developers who wrote Win32 code for retail products or company-internal developers."
Except no one's actually done that for the best part of two decades now. Even before .NET really took off it was far and away MFC that was used for the majority of Windows development. Win32 API development was already largely dead when Gates left for all but the most basic things like setting up a message processing stub to get a DirectX or OpenGL program going.
"However, his middle-empire stage was a shift to focusing on selling to enterprise customers. This isn't a bad things by itself, but by taking his eye off the "Developer!" ball and focusing elsewhere, he guaranteed that plenty of developers went elsewhere."
So what? The enterprise became more important, fat client applications gave way to web applications. Ballmer doubled the profits of Microsoft during his tenure, so it looks like his focus change was exactly what the majority of businesses and developers needed. The fact there's a handful of luddites that bemoan the decrease in usage of Win32 API is meaningless because you're such an irrelevance in the grand scheme of things- most people can deal with change and follow necessary trends, even if you cannot. That's not a problem with Ballmer or Microsoft, that's a problem with you. You can't blame Ballmer's capability for pursuing necessary change for your inability to change.
People shifted to Java because it was a paradigm that gained a lot of hype in both business and academic circles and had a 6 year headstart on .NET and that happened well under Gates' reign not Ballmer's. Mis-steps such as VisualJ++ were the reason for that. By the time Gates stepped down as CEO, .NET hadn't even been released so Ballmer's tenure was the one that was responsible for taking all those devs lost during Gates' reign back because a combination of a far more competitive .NET, and Oracle's screwing of Java has helped grow the .NET community massively.
"It's interesting to see how Nadella is shifting the focus again and broadening it (Windows 10 on Raspberry Pi, for example). Time will tell if Nadella is simply being an anti-Ballmer or if this glasnost is signs of a more fundamental shift in the way Microsoft does business. I hope it's the latter."
It's neither. It's a continuation of the status quo, or did you completely miss that Ballmer also pushed Windows 8 on ARM? This increase in scope of platform support, and move to open sourcing of APIs started well within Ballmer's years. Nadella is just continuing what was already started. It's not a change in direction, it's business as usual as it has been for some time now.