These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Crowning Music Of Awesome: Both games have fantastic scores contributed by Yuzo Koshiro. Aside from being deeply rich and powerful musically, they also sound nearly orchestral—a phenomenal achievement for cartridge based games.
Demonic Spiders: The Skull Head enemies in the simulation sections — they can move fast, cause massive damage to your angel, take twice as many hits to kill as the second-strongest simulation enemy and level your towns with earthquakes if you leave them alone for too long.
Although it's not found until near the end of the game, the Magical Aura spell makes boss battles pitifully easy. It's even possible to kill the arctic wyvern - normally one of the toughest bosses in the game - without taking a single point of damage just by casting magic aura every time he swoops at you.
Also Napper Bats, the first monsters found in simulation mode; a single arrow blips one out of existence, and their large wingspans make them easy targets from the north or south. They are nonetheless annoying because they often spawn from two or three different lairs at once, are very difficult to shoot from the side, and (true to their name) kidnap groups of your subjects when left alone and carry them off, never to be seen again.
Harsher in Hindsight: Causing earthquakes and lightning, etc. to alter the landscape doesn't quite feel the same when compared to witnessing real-world disasters and tragedies, although in-game this isn't seen as sad or tragic at all.
Most Wonderful Sound: The cheery bubbling noise that accompanies the "Town Under Construction" message. It means your city is growing!
In the simulation sections, your angel doesn't die from losing all his HP, but he can't shoot arrows in this state, turning your townspeople into sitting ducks for monsters. However, the angel gets some HP back when the town expands; the cheery bubbling noise indicates that you can once again kick monster butt.
Porting Disaster: The mobile phone port of the first game has horrible controls, no music, only three levels (the final boss being the Manticore), and no simulation mode.
Scrappy Mechanic: Bridges in the first two regions (Fillmore and Bloodpool). If you want to max out your population, in addition to scoring well in the action stages, you need to follow rather strict building directions in order not to waste your limit of 128 buildings, which includes bridges in that total.
Suspiciously Similar Song: The music that plays over the credits has a knock-off of the 20th Century Fox fanfare and parts of the World Tree theme (AKA Northwall Act II) sound inspired by Star Wars.
That One Boss: It's virtually impossible to dodge the Minotaurus' attacks, especially if you want to do any damage yourself.
Unfortunate Implications: Although none of the boss figures actually resemble figures from real-life religions(save for Tanzra/Satan, who as the Greek God Pan was a victim of Real-World demonization centuries prior to this game), it's still a staple of the gameplay that the Master is a jealous God. And, according to more fundamentalist Christianity, any other gods being worshiped either don't exist or are false gods/evil spirits and should be eliminated.
This is as opposed to broader more boundary-crossing and accepting states of worship and/or philosophy, where Jesus is referenced within Hinduism and the Buddha himself is considered to be one of the many Avatars of Vishnu.