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First, if you haven't double checked, make sure you are in T mode. T mode requires a bit more rotation of the throttle to get the same results then when in S mode.
Most of what you are noticing is the difference between Carburetor bikes, EFI bikes and Throttle by Wire bikes. Carb bikes have a very soft throttle, (by comparison), that is very forgiving and allows small hand movements that do not affect throttle action. EFI bikes are more sensitive to throttle movement and have a more precise fuel delivery. Throttle by wire bikes are very sensitive to throttle movement and virtually any rotation of the throttle will cause a change in fuel delivery, thus the twitchy feeling you have.
Most people train their wrist as they ride the bike and get accustomed to it over time. If your last bike was a carburetor bike, the change to the Super Ten's throttle by wire is a dramatic one and it will take you longer to get used to it and master the fine motor control required to be smooth in some conditions.
On to things you can do to help make this easier or better for you. Start with free and easy things before you decide to throw money at this.
I found a BIG help was to minimize the slack in the throttle cables. Yamaha specs a pretty good amount of slack. There is an adjuster nut under a rubber sleeve near the handlebar end of the cables. Pull the rubber sleeve back to get to the nuts. It's a normal double nut arrangement. Loosen the jam nuts and experiment with the amount of slack, reducing it as much as you can w/o impacting the idle speed.
Remember that when you have the bike off there is a small difference between the active slack than when the bike is on. What I mean by this is that the slack will feel good with the bike off and then when you fire it up, it will be reduced and may impact the idle speed. As the servo comes on, it "tightens up" just a bit. Some experimentation is usually involved to find out how much slack you need to not impact idle, but still get it as little as possible. Remember to give the bars a good back and forth swing, lock to lock, to be sure no idle changes occur after your adjustment. I did this when I first got my 2012 Super Tenere in 2011. After riding a Super Ten for 100k plus, I did not find this necessary on my 2015 Super Ten when I moved to a Gen II bike.
Some riders have un-wrapped the throttle spring one turn. You have to be careful when doing this so it doesn't get away from you. There are two springs, if I recall correctly, and they wrap around the barrel at the throttle more than once. Some have reported that un-wrapping one of the springs reduces the 'snap back' action of the throttle and makes it easier to modulate at the grip. I have not tried this.
There are throttle tube kits that allow a cam system that reduces and alters the progressive action of the throttle. It makes the off idle action require more rotation of the throttle tube while still making higher rpm changes quicker. Here is a link to the most common one that I am aware off. Several vendors sell it.
G2 Throttle Tamer Edit: Be Aware that many different cams are available for the G2 and some will make the issue worse! The 400 cam was designed to cure the abrupt initial power delivery.
The Flash that people talk about can alter and improve many facets of the bike's engine and throttle. The standard ones you can buy are only tailored for basic common desires like improving air/fuel delivery to match accessory changes like exhaust pipes, cat deletes, etc. However, a custom Flash done to address the issues you specifically have is available at a reasonable cost and does not have to change other things if you do not want to. Even things like engine braking can be adjusted. One of the forum members offers this and is very experienced in doing them just for the Super Tenere. You may wish to start a private message conversation with
Tony to see if what he can do will be something you may want to consider, but I would try the free things first, one at a time in progression, before you decide to spend any money on a G2 or Flash. The thread
HERE is 23 pages long, but worth reading if you get serious about this, as many answers to questions you may have have already been asked. He's been doing it for a while and has learned a lot along the way.
In regards to your comments about gravel roads and mild first gear climbs. On gravel, changing the traction control, (TCS), to 2 is helpful. (I think that's what Fennellg meant to say since 1 is the default setting.) It defaults to 1 when ever you turn the bike off. (
Remember that when you stop during a ride for a break! ) 2 setting allows some wheel spin w/o getting carried away enough for the rear to step out. It makes things a little more forgiving on gravel and I find that easier for me to be smooth with the throttle too.
First gear. That's what you use to get to second gear, not a travel gear.
The Super Ten's big parallel twin motor has a lot of low end torque. Try shifting up to second and keep your speed in your comfort zone and see what that feels like. You may be surprised and how the bike will allow you to just chug along. It will also make a difference in the throttle response with the taller gear at low rpm. A small throttle movement will result in a less abrupt change in speed and should be less jerky.
Try this stuff and see what others offer as well. If those changes help you while you adjust to the throttle by wire system of the Super Tenere, then you may have no need to go further, but if not, you have some direction to investigate. Enjoy the bike and I hope this helps.