I don't recall being annoyed by those changes. In particular, the VGA->DVI transition was handled really well. Just about everything was DVI-I and would accept a VGA signal over a DVI cable, so you just bought a VGA->DVI cable and continued using VGA.
My school was mostly iMac G3s and I vaguely recall the lack of a floppy drive being annoying once or twice, but the Windows machines had floppy drives and you could easily share files on the network, so it was never a big deal.
On the other hand, I think the most impressive and smoothest transitions I've ever seen in the entire personal computer space were Apple's transition from 68K to PowerPC processors, and almost as smooth their transition from PowerPC to X86. I'm still incredibly impressed with the attention to detail they showed getting those major changes to work so smoothly for users.
Just about everything was USB-C and would accept a USB-A signal over a USB-C cable, so you just bought a USB-C->USB-A cable and continued using USB-A.
I don't see a difference. Except the part where you say the transition was handled well. I didn't feel good applying that to USB-C...
VGA devices always connected via a cable, so you weren't adding bulk. Even adapters for devices with integrated cables (grrr...) were pretty minor compared to the sheer heft of the VGA cable itself.