Just to give my experience - I've had my tomos since new (2000) and put almost 4k km on it so far, and it's been quite the solid machine for me. So far I've had to replace bulbs and some parts of the wiring (metal fatigue on some of the connectors and such, I decided to go with an entirely new front harness just for reliabilities sake) - aside from these (and these didn't show up until after 2500km) it's been a rock solid machine for me.
It wouldn't surprise me however to find the odometer being off - I've ridden a puch, a tomos, and a jawa... and I don't believe any of them were exactly spot on for that (moped odometers aren't usually precise so far as I'm aware.
I think part of things can be the dealer you get (how well they put together the machine makes a big difference, and I have heard horror stories about putting the wrong oil in, hooking up things incorrectly, etc) And like anything else, you occasionally get bad parts - but again if you have a decent dealer it isn't a hassle. In my case they did a recall on a brake issue - just because SOME machines in a batch had slightly longer braking distances - and the dealer came to my house, did all the work, all under the recall so no charge (and I ended up with brand new brakes and cables)
And I've never even noticed a braking issue whatsover.
For the shifting issue - do you have a biturbo or performance exhaust on your machine? They tend to throw off the shifting a bit because they're altering the power of your machine. That isn't bad design, the performance exhaust is changing the stock design from what is intended.
Mind you it's entirely possible you got a crap machine and I got lucky and got a solid one - but I thought I'd give my experience just to balance out the viewpoints (Few too many people saying "I heard this about Tomos" without saying they actually OWN one :)