if these are the only two TJ's you have looked at I would advise to keep looking, just to be sure you get what you really want. did you check the frames and floor pans for rust?
as for transmission choice you cant go wrong either way.
2002 Wrangler Sahara, all stock, 5-speed, Dana 44, dual tan tops, 2nd owner.
2008 Hemi Grand Cherokee Limited 4X4, Quadradrive II, original owner, 24,000 miles.