From what I've heard, getting it rebuilt or a rebuild might not last that long depending on the quality of the rebuild. I've heard more then a few cases where someone gets it rebuilt and it breaks on then again.
If that's the case then it would be better to get a used tranny out of a late model TJ which hasn't been touched. You could even switch over to an external slave if you don't have one already.
Otherwise, the NV3550 is probably the best bet and allow you to do an engine swap later. Same goes for a NV4500.
EXACTLY! Mine had already been rebuilt about 47k miles ago before I bought it. I was driving home from Florida to Georgia and about 100 miles back towards home I left a gas station and chirped the tires in first. About 20 miles later I lost every gear but 4th. I drove the rest of the I guess 400 miles to Lawrenceville, GA in 4th gear only. I only stopped for gas and prayed the whole way that I wouldn't lose 4th.
When I got it apar the insde of the tranny was gernaded inside. It would have cost me so much to replace all those gears, seals and bearings it was better to start over. Ever shop I called said $1500 and althought it would come with a warrantee for a year they said it would prolly let go again because the gears are weak. And those gears are AT least $75 each depending upon which one and I already counted 4 that were missing teeth.
Before I decided to do the conversion I asked on all the 4 forums I subscribe to about how many miles they have on their rebuilt AX5.
I got response anywhere from 5k to 128k miles. Most had let go in the lower miles like mine around 40-50k after rebuild, some where still going after 100k. It's a crap shoot on which one you will get. So I went for the sure thing and did the conversion.
Good luck with what ever choice you make.
It just makes sense to put in a stronger tranny if you plan on keeping the jeep longer than a year.