That or Zack (Pebble's real name) will just go to New York to be with Jon. One of the rumors I hear regarding Jon's leaving is it might have had to do with a strong disagreement on a certain subject and neither have gotten over it, but another common rumor is that there were problems between Jon's girlfriend, Nicole, and Arin's wife, Suzy. Nicole seems to have hinted that, around the time they left LA for NY, Suzy was being kinda… bitchy. No outright verification though, so don't quote me on this.

I heard that Suzy actually hit Nicole for some reason. (Also no verification)
The most compelling theory I have heard is that Jon did not like how Arin was controlling Game Grumps (becoming more business and less "Two friends hanging out", making decisions behind Jon's back including the addition of Steam Train, treating Jon like an employee), and Jon wanted to actually work on his art.
Sadly, it seems that everyone, including Jon, is fine with getting over the split…except Arin and Suzy. Just judging from my own observations and such, that is.
I will personally always prefer Jon because he has integrity and will actually stand up for himself and his art. Arin just…beat-boxes and tells people to "pussy up." Anywho~
Jon hangs out with Spazkid and Stamper (Recent Continue episode thingie), so hanging out with Zack and Oney is not far off. :3