I don't have endo, so I'm not sure how things would work for you, but I had a special dye-xray done which showed that my tubes were badly blocked and filled with fluid.
I was 23 I think at the time and because I had lots of scar tissue as well I was told that the fluid in you're tubes can be embryo toxix and i was advised to have them removed.
It was a very hard thing for me to hear and come to terms with, but ultimately was the best news I could have had. When it came to a final decision there was no contest... continuous pain and possible failed attempts or the best chance I could give my babies...
I decided to have both of my fallopian tubes removed when I was 24, which obviously meant that I would not have any hope of concieving without IVF.... I recovered, and almost a year after I had my op I started my first cycle of IVF.
The choice to remove my tubes was so the best option, because I was lucky enough that the treatment worked, as I now have been blessed with twins - a boy and a girl

.
I can't speak for anyone else, but I felt that my choice to remove the problem just aided my treatment and helped us achieve the family that we wanted.
Good Luck with whatever choice you make.