I was in the same position in 2014, trying to decide whether to go with a new AT or MT. Going into it my strong preference was for a MT. However, after many months of research on the ongoing throwout bearing problems with the RA61F transmission, a careful analysis of the how the TO bearing is guided on the aluminum quill that's an integral (non-replaceable) part of the transmission housing, the fact that the MT is a full-time 4WD, and the knowledge that I would intend to keep the vehicle for 300K miles, I (somewhat reluctantly) went with the AT.
Now, 45K miles, 2 FJ Summits, and countless hours off-road in various conditions, I'm glad I went with the AT. If you lived in an area where you were driving on snow-covered roads 9 months out of the year, the full-time 4WD of the MT would likely be a benefit. IMHO, off-roading where you are picking your way slowly over wet rocks or other uneven, low-traction surfaces, the AT makes it easier to smoothly modulate power and maintain traction (in conjunction with ATRAC).
If the photos you posted are of the MT you are looking at, and it has 125K miles on it with zero history of clutch or TO bearing issues, for whatever reason it may not be one of those subject to these problems. Just be advised that many manual transmission FJ and Tacoma owners have encountered repeated, apparently uncorrectable TO bearing problems. Others have not.
To be well-informed, research the multiple threads on this forum regarding TO bearing problems, then make your choice. The FJ in the photos you provided looks very clean, inside and out. How many previous owners, and is a service history available?