Depends really, I certainly have more faith in the Yamaha than I would in a GS, but many swear the GS is the most reliable bike ever built
Overall they are very similar, I have ridden the Twin Cam back to back with the Super Tenere, and obviously have had time to compare the Tenere to my old 2008GS.
I have also done almost exactly the same mods, Wilburs Suspension, Tony Archer Seats, de-cat headers.
The Yamaha is smoother with a more linear delivery and more low-mid range, and the DOHC GS has a bit more top end and "character" (or vibes if you do not believe in character)
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The Traction Control is far better than the old Aircooled GS rubbish ON / OF / ON power sensation, really smooth and it is hard to detect when it cuts in most of the time.
I prefer the ride quality of the forks and rising rate shock, but miss the lack of dive of Telelever front.
The Yamaha feels better (lighter and more easily manouvred) at low speed, but the GS definately turns quicker at high speed, but the Yamaha gives more feedback from the tyres.
Riding position is almost identical, as is comfort, but the Tenere is far more relaxed at speed due to less vibes, it feels effortless at a ton where the GS feels a bit hurried.
MPG is probably better on the GS at low speed (say sub 60mph) and better on the Yamaha at high speed (80mph motorway cruising)
The Yamaha's clocks give more information - which is just as well as the bloody buttons are a stretch to reach, and the BMW heated grips are much better.
So different, yet so similar.
The new GS and KTM are now playing with the Explorer and look more like Sports Tourers in Adventure clothing, and I am sure both would blast the Yamaha on fast roads if your thrashing them.
In fact I would probably choose the old BMW over the new one if I had to ride a GS