Regarding the frog thing, that's just a simple dungeon-entering gimmick (much like, say, getting a key from a certain townsperson) and not really worth noting by the standards of things RPGs pull.
The three mini-dungeons I can more readily see being annoyed by since they actually impact gameplay, though I personally enjoyed them well enough for switching things up and making you (gasp) change jobs in a game which is about job changing!
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