Why should I upgrade my suspension?
Suspension makes your cornering possible. With a lousy suspension you never feel comfortable enough to really lean it over and get on the gas. With good suspension you can lean way over, get on the gas, do mid-turn swerves to avoid obstacles, and stay stable through bumps. How much faster? - light years.
How? Spend money on shocks and forks. The stock 250 Ninja is comfortable but sloppy, so it's easy to improve.