Well...lowering won't really give you a better ride. In fact, if I didn't NEED to lower the bike for getting my feet on the ground better, I would leave it stock height, just to have the added ground clearance. Mine is stock height in front, with Traxxion Dynamics AK-20 cartridges in the front forks. They are the best, but also the most expensive. The Legend Air gets the back end down enough (3+") when I need it down, but allows me to maintain stock height for riding, or anywhere in-between. IMO, those two things are the best combination for getting lower when needed, and for versatility when two up or loaded because you can adjust the rear shocks with the on board air compressor at any time.
The stock suspension just plain sucks, front and rear. The "air shocks" HD gives you on the bike are NO comparison to a good shock for two reasons...it's a poor shock to begin with, and all the air does is give you more preload to keep from bottoming out...the Showa front fork assembly HD gives you is probably the cheapest, low bid crap you'll find on any production motorcycle these days. Notice how your front end dives when you apply the brakes? It shouldn't do that to the extent it does. In my eyes, it's a safety concern as well as a handling concern. ABS brakes make the safety issue less of a concern, but it's still a concern to me.
These are my opinions/suggestions, depending on what you want to accomplish:
Keeping the stock (full) height:1). Traxxion Dynamics AK-20 Cartridges in the forks and either Legend Air Ride shocks on the rear, or Bitubo 330mm (stock height) shocks on the rear. The first combo is the most expensive, but is also the most versitile, giving the ability to adjust for any load/road conditions, and being able to slam the rear end when stopped/parked, or needing to get better footing. The Bitubo shocks are excellent as well, and less expensive than the Legend system. The down side to any "regular" shock is that you will have to adjust them manually for different loads...generally that will be three settings: one up; two up; and two up and loaded. On the Bitubos, that means adjusting the preload spring and the compression damping knob...you can pretty much set the rebound damping and leave it alone. That will be the case for any non air adjustable rear shock. The regular shock on the rear will not lower the bike at all.
Lowering the rear only(without adjustable air shocks):
Replace the front fork guts with either the AK-20's or the Progressive Monotubes in standard, full height. Bitubo 300mm rear shocks: that will lower the rear approximately 1". Second choice for the rear would be Progressive 940's. Some have used Works shocks for the rear as well, with good results. You will need to adjust them for loads though. The Progressive Monotubes are a much cheaper alternative to the Traxxion AK-20's, but still give good results...light years better than stock. The AK-20's are Warp Drive.
Lowering front and rear 1":
Replace the front fork guts with AK-20's 1" lower cartridges. Next best choice: Progressive Monotubes in the 1" lower kit. Rear: Bitubo 300mm shocks. Second choice: Progressive 940's or equivalent.
I personally would NEVER lower the bike more than 1" (fixed height). You give up suspension travel; you give up significant ground clearance and may drag unforgiving parts in curves, which in turn means your ass might get on the pavement.
Arnott also makes a rear air ride suspension, but get their "best" system. At least one or two people have used theirs with good results, from what I know. I have no first hand experience with their system.