I had issues with my 2006 S50, but was able to have a dealer fix them for me. I bought the bike used, and it sat for a while and the carbs got gummed up. The bike is riding fine now, and I am glad I bought this bike, more than enough power and it fits me to a T.
I agree about a sixth gear, but I am sure Suzuki tested the gears for highway driving prior to bringing it to market. I wish you luck with your problems, and if you get it fixed, have a safe ride.
Too bad about your difficulties. Your dealer should have brains enough to figure out the problems with the low speed missing. Since they don't, I will venture a clue. Carbureted bikes are at a disadvantage when it comes to EPA mandated emission standards. While it is all shiny to assume we will be keeping the air cleaner by jetting as lean as possible, the EPA has overlooked the possibility of owners leaving the enrichening knob pulled out to relieve the "lean staggers". Your problem is most likely that you are jetted too lean on the low speed and idle circuits. If you are not mechanically inclined, find someone who can help you remedy the problem. Usually by re-setting the idle air-fuel mixture, and going one or two sizes larger on the low speed jet, you can fix this problem.
I have this bike, and have to say I love it. I have had no issues with the way the bike runs/performs. I switched to after market grips with better dampening properties (Kuryakyn ISO Flames) and customised the seat, and with just those two changes, I find it to be the perfect bike for me. Customising the seat was necessary for making this bike comfortable for trips, the stock seat was a lot NOT comfortable for duration riding. Also, highly recommend getting the windshield to stave off fatigue when doing distance.