Waiting the additional time helps ensure that the J-Pouch is fully sealed. Only 3 months isn't that bad. I had to wait six months because my pouch had a pinhole.
I had my J-Pouch surgery in August 2011 (Cleveland Clinic Florida) then my original pouchogram in October 2011 where I learned there was a pinhole. They assumed that by November 2011 that it would be closed. I had a pouchogram done at a different hospital (University of Pennsylvania) to save on travel costs and they said it was closed. So my takedown was scheduled for early December 2011. The day before my surgery, my surgeon had an odd feeling and requested that I have a pouchogram performed "just to be sure" and the pinhole was still there. This meant no takedown...I was devastated.
The next day, instead of a takedown surgery, he put in some "fix a flat" glue to seal the J-Pouch and enhance the healing process.
He saved my life and my J-Pouch. If the takedown would have occured, the pinhole leak would have infected my system and most likely "poisoned" my J-Pouch.
So I had to wait the additional three months, pay a ton more in insurance (because a new year) and travel costs, but the takedown went great and I have been living with my J-pouch for 7 months and things have been fantastic.
So while I know that have an ileostomy is not fun, sometimes sooner is not always better. But good luck to you.
Take Care,
John