You should adjust controls and suspension settings to fit your preferences! Only when you feel comfortable in your bike you will be able to excel in your riding abilities.

As soon as you get your new or used bike you should adapt it to fit your riding position comfortably.

a. Suspension
Here, following the instruction  in your owners manual you should dial the suspension accordingly to your riding preferences.  Hard terrain, hill climbs and very technical trails: set your suspension towards the soft end, it will absorb the rugged terrain without throwing you off balance, making your ride easier and more enjoyable.Jumps and fast cornering: set your suspension towards the hard end, it will give you better landings and a crispier control on turns. Always follow the owners manual instructions.

b. Levers
If you ride taking the "correct riding posture" (and you should) and you ride standing up a lot, you may want to loosen up your clutch and front brake lever and tilt them downward! so when you are standing up you will be able to reach them in a much more comfortable position ( not needing to 
twist your wrist that much). Back brake lever: adjust the position so it will brake instantly (when pressed) or give it more play so it will take a longer stroke to start braking..... adapt the travel to your preferences.

Breaking Levers: if you drop your bike (and you will!) you may break the clutch or front brake lever..... to avoid this happening in the middle of nowhere is advisable to loosen the perch, so  the  lever will tilt under impact instead of breaking. Also cutting/sawing the levers a little (one or two inches) will make the handle bar take most of the impact of the drop sparing your lever.

A better way yet is to install Bark Busters, these are either plastic or metal protectors that will prevent the levers from breaking or getting badly twisted.

c. Idle set Up
Most bikes have an IDLE knob/screw that will allow you to adjust the idle of the engine to your preferences.

Also you may consider: when hill climbing or riding rough terrain you may want to set your idling a little higher (more rpm) since in this configuration the motorcycle will be harder to "stall" and thus make your life easier in tight situations. If tackling a long or very steep descent, you may want to turn your Idle "down" (less rpm) so the braking power of the engine will be more efficient and noticeable.

d. Handle bars
Here also you  have a couple of options: is you ride standing up consistently and you feel that your handlebar is too low and makes the standing position a "nuisance".... you may want to lift the bars (a couple of inches will work wonders for the tall guys) adding some supplement at the triple clamp and thus elevating the overall position. This will allow you to ride standing up in a much more comfortable position.

You may also be able to lift the bar a little by just loosening them and moving them up. Do not forget to tighten them up when you are finish adjusting them!

e. Bike Height
Yes, is possible to lower the height of some bikes a lot...... if you do not feel comfortable. Loosening both (upper and lower) triple clamps and sliding the forks up! That alone may lower the bike 2/3 inches depending on the make and model.

Also, if you soften the rear spring compression (follow the manual procedures) the bike will sag when you sit on it. This may give you another inch or two.

This procedure shouldn't take more than 10 minutes, and is reversible.

You may also lower your bike by chopping off a portion of the foam on your seat. This procedure is not reversible!

IMPORTANT: Lowering your bike will reduce "ground clearance" and make your life more difficult on rough terrain.