Awesome And Practical: The Scort again. While it does provide additional firepower its main use is to absorb shots above and below you. This is incredibly useful to the point that some levels and Beam Spam bosses go up many times in difficulty if you try them without it.
Boss Rush: No Mercy has you facing the Meroptican Elite; luckily, each one that falls is another check point.
The Cameo: During the good ending, a series of monuments to heroes of classic shoot'em up games such as Gradius, R-Type, Darius and XEXEX are shown.
Collapsing Ceiling Boss: One of the attacks of the Cyclades boss does this. Also a more extreme example with the Dunarys boss, which is literally a collapsing ceiling.
Continuing Is Painful: While not as bad as certain shmups, you lose roughly 33% of your upgrades each time you die, which is still pretty crippling during a boss fight.
Difficulty Spike: The second stage (Cyclades Liberation), and again later on with the Galactic Inferno.
Do Well, But Not Perfect: If you beat the first two phases of the Red Eden boss too quickly, then you'll have to wait forever on the last phase before you can even attack, due to the badly designed movement pattern.
Dummied Out: The game data contains sprites for a monster called Charybdis, which was presumably supposed to appear in the Path of Scylla.
Excuse Plot: There are sixteen lines of dialogue in the entire game, including multiple variations and the post credits scene. And some of those are not even relevant to the plot, whatever it is.
Guide Dang It: A few of the secret items are rather... unintuitive.
Heel-Face Turn: The boss from the two Breather Levels rescues you at the end after your ship is damaged by the collapse of Meropticon. In the best ending, he takes his child to visit a monument to you.
Infinity+1 Sword: Ancient Sword, the last power weapon. Strangely for a shooter game, this is also a literal sword.
Load-Bearing Boss: The entire planet of Meropticon starts self destructing inexplicably after you defeat Hydorah.
Orcus on His Throne: Hydorah's units are attacking but he himself doesn't seem to be doing much besides sit on a throne.
Though since Hydorah has "seeds" maybe it should be her throne.
Marathon Boss: Rubina, if you use anything besides the Wave (which you get much later in the game). Also, if you finish the first two phases of the Red Eden boss too quickly, the third phase will take ages because the timing of the patterns gets messed up.
Also the Galactic Inferno. After a long level and two minibosses, the final boss has three forms (not counting its turret defences), including coming back for some Bullet Hell fun after apparently being killed off. You will be very satisfied and reassured when it finally burns away to nothing.
Shout-Out: Beside the evident inspiration from several classics of the Shoot 'em Up genre (Hydorah looks almost like a lost Konami game from the early 1990s), there are also a couple of references to Turrican: one of the special weapons is an energy wall named "Turri Wall", and the parade of bosses of No Mercy includes the iconic giant fist.
And besides the homage to shmup heroes described above, the game features Yomar◊ from Maze Of Galious as a background element at one point.
The Dev Team Thinks of Everything: Rather than exploding normally as on land, your bombs will simply make a splash and disappear when dropped into the waters of the Path of Scylla.
Waiting Puzzle: The third secret requires you to randomly wait a while in the boss room after defeating the boss.
Wave Motion Gun: You'll be on the wrong end of one of these in Galactic Inferno.
Womb Level: A borderline example with the final segment of Meropticon. The walls appear to be pulsing blood vessels, and everything is red, but it's not clear whether you are actually inside an organism.
Further evidenced by the hydorah seed in the Path of Scylla which is starting to fill the surroundings with the "grasses" seen in the final level.