The suspension comments are good ones... I am a fat guy, 5'6" and 250+. The stock fork setups just aren't for me (springs and dampening) - suspension set-up is what connects you to the road; it dictates the feel and comfort of your ride. When you grab the front brake, the nose will always dive (it physically has to), but spring rate and dampening is what controls the amount of dive and the time to re-center. There is a limit to how much you can adjust the forks or the shock - you can only compress or release a spring so much - this is why spring rate is driven by rider weight and riding style. The idea is getting the optimal range of travel for your suspension and then tuning to set the "feel" that you prefer. My opinion is that a lot of people buy farkles and go faster stuff, but the suspension and brakes are often neglected.
We mod our bikes based on our preferences - but to me, the first thing that any rider should do is set-up/adjust the suspension. Why? Because dialed in suspension will change the feel of the ride, which affects confidence in the ride. It will change the bike's dynamic during acceleration, deceleration (especially sudden events), handling feel in corners, etc. I would liken it to cooking. Adding salt to the recipe can create a better taste than adding salt after the fact. If you try to dial in the suspension and you find that you don't have the right range of travel/stiffness, then you can change the springs for a relatively low cost. After you see how the bike feels in its optimal settings for the ride, then you can determine how far you want to go with the brakes. Do you just need new lines? New pads? New levers or new M/C? New calipers?
The problem with suspension is that it is easy to determine how well a bike stops, based on grabbing a handful of brake and seeing what happens. You can decide if you like the stopping distance, wheel locking, etc. But, if you have never seen how a well tuned suspension feels, then you don't know what a difference it can make. I have seen guys tune suspension for between $35 and $75 - I will say that it is the single best mod I have ever done. My recommendation is to get the suspension set up FIRST - then based on your budget, build the brake system that you want. I have full ohlins on both of my Busas (Gen I and Gen II). For my money, it is the best possible investment in either bike. Your bike's suspension is your bike's core. If you want to lift a lot with your legs, your core comes into play. If you want to bench a lot, your core comes into play.
Your brakes, no matter how good and expensive the brand name, will never stop the bike as well as they could or should - if your suspension is all out of whack.
Just my .02