On the front the 650 has a double clamp triple tree set up like you see on most conventional motorcycles. The 400 has a single clamp set up like you see on most smaller scooters. That difference means the 650 front end is stiffer and has less flex than the 400.
At the rear the 400 has a single shock setup while the 650 has a dual shock setup. Normally the single shock setup would be an advantage because it reduces unsprung weight. However on the 400 the engine and CVT are on the rear swingarm and move up and down with the rear wheel. So they are unsprung weight that more than offset the gain from the single shock setup and negatively affect handling. On the 650 the engine and CVT are mounted in the frame and do not move up and down with the rear wheel.
In practical terms the main place you will notice the difference is when you hit pavement irregularities in corners. Those irregularities upset the 650 a lot less than they do the 400.
Transmissions are very different on a fundamental level.. The 650's CVT runs a gear assembly to drive the rear tire while the 400 has a more conventional (replaceable) belt for final drive.. While the 650 CVT is more polished it is also carries higher maintenance costs.. I think the 400 makes a better 'city' bike and the 650 makes a better 'touring' bike..
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