My secret is not making jokes or critiscizing other users' posts.
Also, elaborate. I see nothing wrong.
Aha! Okay, well, let's break this down:
1.09.4: Complete the game three times. An easy way to do this is to complete the game once, go into level select on that save, and playing ERZ3 two times, which will count towards the completion.
ERZ3 is not in SRB2 v1.09.4. You can, however, use the level select (or a save file) to replay and beat CEZ3 repeatedly in order to fulfill the required number of clears.
After that, you fail to mention everything else you need to do in order to actually get somewhere. Beating the game three times allows you to trigger an event at GFZ1 by jumping three times on the roof of the first house in the level. RedXVI comes out, complains and punishes you by killing you and sending you to an unfinished version of Red Volcano Zone 1. (If you're playing in Ultimate, it's wise to pick up the 1-up further into the act before you trigger Red, because he'll shave off your only life otherwise.)
This is but one of the secrets. There are two more.
Speaking of Ultimate mode, you need to beat it at least once to go any further. Though I think 1.09.4 was dumb in that you could pick Ultimate from the level select, so you only really needed to beat CEZ3 with no rings. Ultimate is unlocked by clearing the game in Very Hard, mind.
The next step requires you to get to GFZ2 with all 7 emeralds. The easiest way to do this would be clearing the game once with all the emeralds, then using the level select to pick GFZ2 and keep your full emerald count. I suppose you could also finish with 6 and then use the level select to pick GFZ1 and get the last one there, but why you would do that is beyond me.
There is a small house hidden in GFZ2, identical to the ones in GFZ1. It is located at the edge of a tall cliff near the first star post, and requires some degree of exploring to get to, at least with Sonic. IIRC, the house dissappears in modified games, and it has been removed from 2.0, too. (Why?)
Touching the door of the house will only reveal an "out to lunch" note, so now Sonic must find where Red is picnicking. Well, it's not that hard (though I was a bit stumped back when Penopat, JTE and I were keeping ourselves busy by immediately trying to figure out the secret as soon as 1.09.4 came out), just backtrack to the start of GFZ2 and you'll find RedXVI on a bright checkered blanket right on the first tall cliff in the stage. Use the nearby spring in the water to reach him.
Approach Red and he'll attempt to make you go away by bribing you with the eighth, black emerald. Since you had the other 7 emeralds under your belt, this means you now have all 8 and can play as Hyper Sonic! Due to where you get the black emerald, you cannot use Hyper Sonic in GFZ1.
The final secret simply requires you to keep playing the game and bring the black emerald to CEZ2. This is the only part of the secret I can really take credit for finding, but even then it wasn't without JTE's help, who gave me the right map number to work with. Jump inside the pool at the center of the stage and Sonic will think to himself that something doesn't feel right. Complete the stage as normal, and you'll find RedXVI at the end of the stage, in place of the sign. With his last ounce of anger he teleports you into a small room beneath the pool, strips you of your rings and sends a pack of Crawla Commanders right in your face. A simple spindash can deal with them, and once you escape the pool and land back on dry... land, the game will notify you've unlocked the "god menu" (read: Pandora's Box) and end the stage.
...Now, where were we?
2.0.6: Complete the game once with all seven emeralds. An easy way to do this is complete a save file once with Tails and then going into level select, and going through the levels again and again until you have all 7 emeralds.
You do not have to complete the game in order to find RedXVI in v2.0. All you need to do is reach CEZ2 with all the emeralds, which is more than doable. There's 1 token in GFZ1, 2 in GFZ2, THZ1 and THZ2, 1 in DSZ1, 3 in DSZ2 and 2 in CEZ1, I think. That's 13 chances at the special stages, and you can get all the emeralds as early as THZ3.
Then you go into the library in ERZ2, where RedXVI is.
Not only is there no library in ERZ2, there's no real library at all in the game. (Except that one screenshot Mystic has revealed of some future architecture in CEZ2(?), not available in any current version.)
Bring the seven emeralds to CEZ2 and be sure to take the top path: when you first reach the inside yard (which should be instantaneous because the gate opens automatically when you have all the emeralds), use the nearby chain to launch you onto a higher ledge and continue through a tunnel. After you press two switches, you'll open the door to the room with the spinning polyobjects, where you'll find an extra exit which leads to a small chapel. The first time around, Pope Rededict XVI will apologize for his past actions and this time send you to heaven, instead of hell. This isn't great news for you, because you'll be sent to Neo Aerial Garden Zone, which is a pastiche of the Aerial Garden, Starlight Palace and Inner Sanctum Zones from Mystic Realm 4, along with lots of brand new content. Clearing this stage will unlock NAGZ for free play in the Secrets menu and send you on your merry way to Arid Canyon, the next stage in line.
Return to CEZ2 and perform the event again after clearing NAGZ once and the good Pope won't repeat the stunt, and instead award you 9999 rings in celebration of AJ and Amy's wedding, which is worth a few 1-Ups on the spot, and a lot more if you manage to carry them to the exit, which is right around the corner.
In short: yes, you clearly missed something.