I think the behavior of flyspell-correct-word should be extended to a command that corrects all occurrences of the misspelled word of interest. This of course is not relevant for syntactic errors in the underlying spelling correction. I don't know if aspell/ispell supports such kinds of corrections. It would also like to combine the two into a command that queries the user whether he wants to correct next occurrence in a query-replace manner (y,n,q,Y,N,!). Has anybody implemented any of these ideas?
Try adding the following code to your .emacs, this seems to do what you're requesting (though it does not prompt you for replacements (that seemed a bit cumbersome)):
(setq flyspell-insert-function 'flyspell-insert-and-replace-all)
(defvar flyspell-last-replacements nil)
(defun flyspell-insert-and-replace-all (word)
(unless (eq flyspell-auto-correct-pos pos) ; same check as done in flyspell-auto-correct-word
(setq flyspell-last-replacements nil))
(save-excursion
(dolist (word-markers flyspell-last-replacements)
(delete-region (car word-markers) (cdr word-markers))
(goto-char (car word-markers))
(insert word)))
(insert word)
(save-excursion
(let ((do-replacement (not flyspell-last-replacements)))
(while (re-search-forward (concat "\\<" flyspell-auto-correct-word "\\>") nil t)
(replace-match word)
;; and, when doing first search/replace, record all the positions
(when do-replacement
(let ((end-marker (point-marker))
(begin-marker (make-marker)))
(set-marker begin-marker (- (point) (length word)))
(set-marker-insertion-type end-marker t)
(set-marker-insertion-type begin-marker nil)
(add-to-list 'flyspell-last-replacements (cons begin-marker end-marker))))))))