When you throw an ender pearl into a Nether portal, several outcomes are possible. Sometimes it gets teleported to the opposite dimension, sometimes it goes through, and sometimes it simply disappears.

Steps to reproduce:
(You need to have a helper observing on the Nether side.)
1. Create a demo world and get into Creative mode. Build and activate a Nether portal. Position the helper in the Nether.
2. In the Overworld, at various distances from the portal, throw an ender pearl toward it at various vertical angles.
3. Repeat the experiments, throwing from the Nether side.

Expected result:
I'm not certain what the intended behavior is, only that it's probably not as variable as the experiments show it to be.

Actual result:
1. If the pearl touches the inside of the portal frame, the player is teleported to that position, after which the portal teleports them into the portal in the opposite dimension. This is probably the intended behavior in this situation.
2. If thrown at a downward angle, or presumably if the portal chunks haven't yet been generated on the opposite side, the pearl disappears.
3. If thrown at an upward angle from 5 or fewer blocks away, the pearl usually teleports into the portal in the opposite dimension, flies off, and despawns before touching a block. The thrower is not teleported. (There is a chance that the pearl will go through the portal instead.)
4. If thrown at an upward angle from 6 or more blocks away, the pearl usually goes through the portal as if it weren't there and teleports the thrower to where it lands.

More information:
On result #3, the pearl appears at the bottom of the portal in the opposite dimension regardless how high it entered the portal at in the origin dimension. The angle it flies off at seems to be proportional to how high it entered.