IMO the "correct" way to handle this is with vanilla vim's built-in macros. Find the next match, record a macro making the edit you want, then find the next match and finish recording the macro. The macro starts with the cursor over the match you want, the edit can be more complex than a simple replacement, and skipping is simply a matter of pressing `n` instead of `@@`.

Vim can also take a command that yields a list of filenames as a launch parameter via something like `vim $(ag -l target_string)`, letting you go through each file with a `:n`, letting you complete large refactors surprisingly quickly.