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.
Big Lipped Alligator Moment: Because the arcade version leaves out most in-game dialogue and cutscenes from the Saturn version, a number of these moments happen for arcade-specific players.
For example, when fighting against GEDO-O, everything turns into a pseudo-Retraux-style wireframes complete with beeps. In the Saturn version, a small in-game cutscene occurs just beforehand where Tengai orders Creator to analyze and record your fight with the GEDO-O. The change to wireframe is concurrent with the start of the recording.
Breather Boss: Nasu is a relatively easy boss after Golets and before the dodecagon which transforms into a cross.
Nightmare Fuel: The Stone-Like destroys all life on the planet...and there is nothing the heroes are able to do about it. They come back to Earth after escaping its destruction, and their entire Last Stand was for NOTHING. Repeat ad infinitum.
Chaining. To elaborate, you rack up points by shooting enemies of the same color; for every three consecutive same-color enemies destroyed, you get a chain bonus; successive iterations will yield larger bonuses, up to 100,000 points per three enemies. This is a source of headaches for many and makes the game extremely difficult even on Very Easy, because:
You must leave roughly 2/3 of enemies intact, and enemies will often be firing at you or presenting collision hazards.
If you destroy so much as one enemy of the wrong color, the entire chain resets.
Weapon levels are tied to your score, and you NEED to power up weapons to keep later bosses from going on for too long. Therefore, mastering the scoring is nearly mandatory to survive.
The Xbox Live port, while far from a Porting Disaster, has an issue with aspect ratio: The game runs in a 4:3 window pillarboxed into a 16:9 screen. This entire layout is then letterboxed if you're playing on a screen with an aspect ratio taller than 16:9. This is practically an insult to those who wish to play on a 4:3 screen, especially a CRT screen just like with the Saturn and ST-V versions.
To unlock Ikaruga mode, you need to have played Ikaruga and earned at least one achievement under the same account you use to play Radiant Silvergun. Unless you have an acquaintance who has the game, this amounts to $10 DLC if you don't want to play Ikaruga or already have another version of it.
That One Boss: The third boss, Gallop, is already packing a big punch with a large variety of attacks.
DAIKAI10 in Stage 2 transforms into a cross shape and back, filling the two corridors it creates with laser beams.
Or the part where you have to fight against a series of battles against numerous small robots and you'll get surrounded by five planes.
Ohtrigen can cause more deaths per minute than any other boss in the game.
That One Level: Evasion. Probably the most difficult stage in the entire game in terms of multiple obstacles and hard to dodge attacks from bosses.
For those who want to get large chains, 5A is probably the most challenging one and it takes place during the boss fight. There are tons of drone ships flying around and the second phase of the fight has kamikaze ships flying at you, wall turrets firing at you and at the same time, walls like to periodically close in with a huge missile flying through, girders slide through the corridor and eventually the whole boss starts rotating. Hit a wrong enemy and the chain is reset.