Bogis' Problem
 

In this last quest of frogmen trio I have two options how I would like to complete the quest:
A. put the flag of eldest brother on two houses of younger brothers
B. attack eldest brother and put king's flag on all three houses

Choosing option A gives quest reward and additional troops/items to buy in frogmen's houses.
Choosing option B gives quest reward and.. nothing else?

Yes, option B gives also some experience for fight with eldest brother but is this the only one additional gain?

I don't remember anymore...if you defeat him and raise the king's flag, do the items/units not change, then? Unless you were counting on a supply of royal snakes, I don't think it's anything worth fussing about. :)

The items and troops have already changed by the time you do Bogis' problem. The change in lineup happens after the prequest to that where you have to subdue Bagaba in favor of Squelch. He's also the one who has the Royal Snakes.

Conclusion: raising the King's Flag gives you additional XP and one more battle ---> win :>

I think it is not true? Scanner shows that some units/items in frogmen castles have condition: "Complete the Quest Bogis' Problem in Favor of frogus Bagaba". Last time I've checked it was true and these units appeared only when I flagged two castles of younger brothers with elder brother's flag.

I'll check this later today again.

I know what the Scanner says. Not with me. The units always change after Subdue Bagaba already and no matter how I solve Bogis Problem, they all stay the same.

I've checked these both options and, indeed, all shops grow bigger in any case*. But new units/items are available after finishing Bogis' Problem, not before as you said.

*) I think it could be some unintended and uncorrected bug.