Imagine copying via Ctrl-C and having to hit enter to confirm a dialog "Did you want to copy this text". It's added, unavoidable friction for an action that some people use a lot.
Additionally, some actions on top of the original behavior (that depended on Ctrl-C completing automatically, to keep with the analogy), now are just broken.
While I appreciate the analogy, it's important to note that registers are a fairly advanced feature, not quite as ubiquitous as Ctrl-C. Standard Emacs copy-paste remains unchanged and functions just as expected.
I also don't really use emacs. But by the sounds of it, when you want to use a command that involves a register, you get a mini-popup where you input the register you want.
The downside is that you must push enter after you enter the register you want.
Additionally, some actions on top of the original behavior (that depended on Ctrl-C completing automatically, to keep with the analogy), now are just broken.