It's not that it's too hectic - I can deal with the bullets just fine, but the system just wasn't making sense to me. I played a bit more and the gems go up to 500 while the gold goes up to 1000. So, from what I can gather, the system exists so that you can get a maximum of 1000 (x 100) more points than if you just tried to collect gold. But still, you have to spend gems to get gold, and not only that, the gold depletes pretty quickly during boss fights. Just seems weird to me.
Assuming were talking about Arcade and 360 Mode:
You collect green gems in Normal Mode (bullets are blue) by killing enemies. The closer your proximity to an enemy when you kill it, the greater the number of gems you receive (also you're awarded more for using autofire than using rapier). Gem collection maxes at 500. Any enemies killed while gems are maxed will drop gold.
Gems allow you to enter the various Kakusei Modes. Tap the Kakusei button to enter standard Kakusei mode ("bullet time" mode, bullets change to pink). In standard Kakusei, enemy fire can be cancelled into gold. Simply allow an enemy to build up a load of bullets on screen and then kill them to turn all of their bullets into gold. Gold grants up to a 100x multiplier per unit (this multiplier resets each time you exit Kakusei). Gold collection maxes at 1000. Gems will steadily deplete in Kakusei Mode, although each time an enemy is destroyed, a percentage of gems will be removed depending on the volume of bullets cancelled.
In order to enter Kakusei Zetsushikai (from here on in abbreviated "Zetsu"), you will need both gems and gold. Press and hold down the Kakusei button to enter Zetsu Mode. When in Zetsu, killing an enemy cancels theirs bullets, however these bullets will then respawn into new bullets. Killing another enemy will cancel all respawned bullets and cause then to re-respawn. Cancelled respawn bullets grant up to a 500x multiplier. This mode is where most of the game's heavy duty scoring is done. Both gems and gold will steadily deplete whilst in Zetsu Mode.
If gold reaches 0 before gems do, Zetsu will instantly revert to standard Kakusei. At this point, killing any enemy will permanently cancel all on-screen respawn bullets (with a max multiplier of 100x granted per bullet).
Should you run out of gems whilst in either Kakusei Mode, you will enter OverDrive (bullets change to red). In OD bullets speed up. There are 3 levels of OD, designated by a blue meter that surrounds your character. Each time the blue meter completes one circumference of your character, the game rank increases. The percentage of gems for killing enemies in Normal Mode increases with the rank (this is why players will max the rank out in the first stage, so that they're pulling max gem counts from enemies for the rest of the game). Whilst in OD, all destroyed enemies drop gold.