Are you sure YOU know what Gengtsu rape time is? As No Name said, it's the timeout phase, which you would never normally have to fight. Ordinarily it's just a pretty mild spell, and the rest of her spells are dementedly easy so she's by far and away the easiest extra boss in the series (yes I've fought them all). And despite the easiness of Gengetsu, Mokou is generally held to be the easiest, so I don't see why you think she's harder. She actually has only one spell that takes any dodging, eveything else is memotrash. And the low resources on Flan are a source of difficulty, not an indicator of the bosses weakness. And how is Kaguya a joke boss? She's up there with Remilia and Byakuren I'd say. On Lunatic at least.
I think that when taking a boss into account, you should look at every of her aspects, which is why I included gengetsu's rape time. and well, you cannot deny that it's by far the hardest thing ever in touhou :s
I find mokou difficult, very much so. she has one of the hardest non-spells in the whole series, fujiyama volcano is generally accepted as a very difficult spell, and I have seen many many people who have trouble with her timeout spell for several reasons.
yes, but the amount of resources you get are an indicator of how strong the boss is. I think that if she was on a higher level, then we'd have gotten at least one more life somewhere in the stage, as to keep the extra stage and its boss on a "around hard" level, which is what extra stages are. of course having less lives and bombs makes a stage harder, but in retrospect, it also shows that you don't really need more as an averange (or little above) player to beat the stage. I believe that you get as many resources as you need to win an extra stage when you are somewhere between normal and hard, which is why you only have 5 lives altogther in EoSD. the only exception is SA, because the life giving system is very...default.
as for kaguya: yep, she's hard as crazy on lunatic, but you see, not very many people play her on lunatic. most people are around normal and therefore fight kaguya on normal, in which case, she really is a joke. the difficulty jump from hard to lunatic is very steep in her case, moreso than for other bosses, in my opinion, with the possible exception of kanako (who I find to be among the most difficult stage 6 bosses on lunatic, but that'S another story).
another extra boss who is definitely harder than Flan is marisa. GFW might not be a main game, but it's still a regular shooter with merely a special gimmick, after all. I suppose thinking about marisa makes me want to take back what I said about gengetsu for being the hardest, but I'll leave it at that.