That is a very hard decision. One that is very personal with different variables for each person. I had to make that decision too. I have had IBD since 1996. Originally, the doctor thought it was Crohn's. Last year, I found out I had colon cancer, which everyone with IBD is at high risk for as time goes on due to inflammation in the colon over time.
Thus, my decision at the time of surgery was to choose permanent ileostomy or J pouch. Many surgeons won't do a J pouch if you have had a history of Crohn's due to the increased risk of inflammation in the J pouch and associated issues. I had my colon and rectum removed. If you don't have a history of inflammation in the small intestine but have Crohn's, some surgeons will allow a J pouch, but many won't. Cleveland Clinic has statistics that say if the Crohn's patient doesn't have signs of inflammation in the small intestine, 85% of those patients successfully still have a J pouch 10 years after surgery. Patients with UC have a 10-year success rate in the 90-94% range. I decided to go with a J pouch if my surgeon would let me. On the operating table, the surgeon looked closely and did not see inflammation in my small intestine, and actually changed my diagnosis to UC based on what he saw directly. Thus, he did the J pouch on me.
I had a temporary "loop" ileostomy for about 9 months before having my "takedown" hooking up to the J pouch and closing up the ostomy. I am now 2 months post-takedown. Keep that in mind as the basis for my opinion - not a long time with either but more than you have experienced.
Ostomy Pros:
1. Less risk of future complications, namely pouchitis.
2. No risk of cancer in the anal transition zone.
3. No J Pouch second surgery with recovery.
4. No risk of having to have the J pouch removed later, which is a very involved surgery.
5. Won't ever get pouchitis, IBD-like condition in the J Pouch.
6. Technically don't ever have to sit on a public toilet again, although kneeling on the floor in a public restroom seems worse to me.
7. No bloating - no pressure on your system as it all goes into the bag. With J pouch, I do have bloating, etc., more of that type of discomfort. That may be because I am only 2 months post-takedown and I went 9 months with no pressure in my system. But it is a J pouch drawback for me right now.
8. No irritated skin around the anus from stool going past it often every day.
J Pouch Pros:
1. No bag for me has meant more physical comfort and ability to do activities easier - swimming, sex, running, etc., despite the positive spin some people have on doing those things easily with the bag. I was leery of running as I worried it could loosen the wafer from the up and down.
2. I always worried about the bag being too full and would want to check it. J Pouch you "feel" how full you are and know that way when to go.
3. Much less risk of hernias. Your abdomen is simply more physically sound.
4. For me, just a more natural way to go to the bathroom. As my surgeon put it, "Do you want to poop out of your side or your butt?" Either answer is legitimate in our situation.
5. No morning wafer changes like needed with the bag. I was slow at that and I hated doing it.
6. To me, emptying the J pouch is easier than emptying the bag.
7. No irritated skin around the stoma from wafer leakage, etc.
All considered, I am glad so far I went with a J pouch with J Pouch Pro #1 being weighted more heavily by me. I recovered fairly quickly and am averaging going #2 six times in a 24-hour period. At month 2, that is better than average. Ask me in a year and a week when I may have pouchitis and maybe I give you a different answer. But I didn't want to go permanent and not give the J pouch a try. The extra surgery risk was worth it for me. But I never had surgery before my colon cancer. Others have had more surgeries and other health issues, so more surgery would be a bigger deal for them.
Hope the above helps. I am sure I could share more, but the above are my first thoughts on the matter. Good luck and remember perspective. It can always be worse. Without either option, we wouldn't be alive or maybe going to the bathroom 20 times a day.