This is interesting—I hadn't heard of vis or Sam. Thanks for sharing!
I will say that I like to think of myself as a reasonably advanced Vim user, and the substitution commands used for the example wouldn't have even occurred to me for changes 1 and 2. I would have automatically done it the alternative ways listed. I'm pretty sure those would be faster to type too (they're fewer keystrokes). Is it really true for most people that "the substitute command is used 90% of the time when using commands"?