Righto, after much thought on the matter, this is my theory on the Portal.

The portal is only known to sorcerers and dieties, few know it's location, even fewer know how to use it. To travel through the portal, you must defeat a representation of your greatest adversary. The portal is the means of travel through the realms.

Ok, let's pull that apart:

You must defeat a REPRESENTATION of your greatest adversary. Therefore, as Arcade is played in first-person (ie you are the character), you cannot travel through the portal in arcade. In 2 player mode, remember it is player vs player, not character vs character. Therefore, the representation is applicable.

Even fewer know how to use it's power - meaning either of two things:
1) Only sorcerers and dieties can activate the portal, seeing as they only know how to use it. Meaning you must either play as Shang Tsung, Quan Chi, or Rayden to go through it.
2) You must enter a button combination during "Finish him" to travel through it.

"The portal is the means of travel through the realms." - The one arena we have no idea about, and we see being created in MK:Unseen is the Senate of the Elder Gods. Remember it is in another realm, as the Elder gods do not go to other realms, and Rayden had to travel to see them in MK:A. The fact we have seen it being created in full means that it should be in the game.

Other things worth noting:
"Time will lead you to Saibot" - you must fight at the portal during a certain time of day to activate it, where you are transported to the Senate to fight Noob Saibot.

"People have hacked the game" - I've yet to hear of what is in the .pak files. As far as I know, nobody has been able to open them.

Hope that gives people some direction in their hunt for the last secret.