I think doctors who don't have enough J-Pouch patient experience tend to say remove the pouch. Most GI docs don't keep updated on the care options for us J-Pouchers. I can't tell you how many doctors I have been to, including GI doctors, that have never even heard of a J-Pouch. I'm 28 yrs with a J-Pouch and the last 16 yrs with added fistulas. Only with the added fistulas did my GI doctor suggest removal. I always have inflammation in my pouch, some days tolerable, some not (then I take 2 Aleve/day for a couple of days). Didn't like the treatment options for the fistulas - they would never go away, they just become another thing to maintain so I took a pass and deal with them.   

I had an iliostomy for 4 months prior to take down, for me personally, was not a fan of it. Would rather have my pouch over an iliostomy bag. When I went to Cleveland Clinic and Loyola Hospitals for information on Pouch removal, one surgeon refused to remove it because of the high risks involved - but was never told what they were - so frustrating when docs ignore questions. The other surgeon proceeded to tell me about their "new findings" regarding pouch cancer starting to show up on patients who had a pouch for 20+ years and that it was very aggressive with not a good survival rate. Probably, for me, the most important reason to remove the pouch would be for this cancer finding, but would not answer me when asked if I should remove it.  Refused to advise me on what his recommendation would be. 

My GI doc is great, always tells me the latest meds and findings, but is very up front and honest when I ask him if it is worth the risk of the side effects that come with them - almost always tells me no. Sometimes older meds are safer than new meds. 

Has anyone had their J-Pouch removed after having it long term? 

Risks of pouch removal: bleeding ,necessitating re-operation, damage to adjacent structure such as bladder, ureter and other loops of bowel.

I had mine removed at the Mayo Clinic with no post surgical problems other than the usual incisions healing, abdomen and back door, and getting use to a permanent ileostomy.  I was told the surgery was more difficult for doctors than the j-pouch surgeries.