How Shout-Out examples are linked together. For example, Nevras's status as a crossdresser is already a Shout-Out to Cloud's own scene. It is later merged with another reference, that of the Lotus combo technique, except it is called Blossom, and instead of a Lotus (usually the symbol of the Buddha), it is based on a picture of a Crysanthemum, the symbol of femininity. Let that sink in for an ultimate attack of a male character.
Normally, Strawman Has a Point would be a criticism of a story. But this is almost the point of the story, that everyone has a viewpoint that is valid. The "villain" of the story in both cases is shown as extremely sympathetic, even if they are clearly intended to be a villain.
As are the recurring sidekicks.
Ambrosia's voice. Her personality is Mood-SwingerKuudere, with some Tsundere, and some Cute and Psycho moments. How do you make a character who shifts the spectrum of emotion, but still comes out sounding emotionless under the surface? And yet, her voice actress managed it...
Lilith's voice is fairly normal, but "seductive" and is supposed to be a demon. What else was supposed to associated with evil? They call it Subliminal Seduction, or backmasking. Therefore, in her normal lines her voice is taped under as backmask (interestingly, it sounds more like Russian or French than some evil language ).
First, we have the Money Spider trope typical of Rpgs, which was available in the original versions. This has largely been averted, replaced instead with Vendor Trash, Adam Smith Hates Your Guts, and Continuing Is Painful (where you lose half your gold if you die). When you finally do manage to get and keep your money, weapons and armor are either absurdly expensive, you have Money for Nothing. But then, this is reconstructed when it turns out you can use banks to neatly avert many of these problems. This actually makes the economy somewhat more realistic (from a fantasy perspective anyway).
Then we have the Romance Sidequest popular on everything from the Final Fantasy series to several others. Only, the hero's sidequest in this regard can end with you getting dumped, and then you either try to patch things up, or Ambrosia has a fair amount of Wangst for the rest of the series, followed by pretty much all the endings being a Downer Ending. The secondary characters also have the option for a romantic events, but here, things pretty much start with a rather massive test of trust, since one of the lovers was drunk at the time, and may or may not have had a lesbian affair. Whether this turns out to be true or false, whether the relationship above is patched or not, each option is fleshed out to improve upon the original romance (unless, of course you skip half the scenes).
The Happily Ever After ending (for that matter, the Standard Hero Reward). Even the best ending has some serious Fridge Horror going on (with the threat of an actual Dream Apocalypse), before the characters ultimately choose a quiet hut in the outskirts over the idealized reward of a castle and kingdom. By the end of the second game, the Fluffy Cloud Heaven is mocked, and instead a Mundane Afterlife is put forward as an actual acceptable substitute (considering the implications of Heaven being a torment of extreme and eternal boredom). The fact that the two can basically leave Heaven whenever they want averts this, creating an afterlife that, while not perfect, is at least tolerable.
Ambrosia's Oracle powers in the first game have a few limits, like not being able to be used two turns in row. She becomes God after the first game, and in the Endgame Plus she can use her powers at will.
See the Ascended Fridge Horror section on the main where none of the characters really exist... Now extend this to Real Life. How can you be sure those you know are real? Sure, you can touch and speak to people, but consider the film A Beautiful Mind where the lead is fully convinced those he hallucinated are real.
In the "best ending" of the second game, she decides to just leave Estheriel alone, and enjoy what's left of her life. This is viewed as a neutral option, compared with killing him, and saving him. But consider this, Estheriel has just been Impaled with Extreme Prejudice, and not only is unlikely to recover, but also die a very painful death without intervention from her. Even killing Estheriel is a better option than doing nothing. And considering that killing Estheriel made her crazy, it's hard to believe she can just walk away like that.
Think about Ambrosia for a bit. A Cute and PsychoKuudere who gets mood swings. Now, as part of the story, she becomes God. Would you really want someone like this ruling the universe?
What were Sera and Phim doing up in the mountains hunting wolves when they had a key to a temple (well, not like there was much of anything valuable there)? For that matter, how did they end up in half the places they showed up in (the Void? It might as well be the moon)?
Ostensibly, the world is set in the future from Earth's own destruction and recreation, and there is a different time system (there are thirteen months). But after the world becomes real again, time reverts back to what it was before.