As to what is better, trip. or twin, that is up to you. Everyone has a different opinion on that and only you can decide. Test drive both if given the opertunity and come to you own conclusion.
I personaly prefer the triple/triple sleds, but others sware by the twins.
As for the '99 zert 600, it's a good sled, but the '95-'98 models have better performance in stock form. Cat seems to make all their new trips into touring sleds when they come from the factory. You can make the sled perform much better than stock though once you start playing with the clutching. All in all, if you are used to triples, the baby zert is a great sled with allot of potential.
As for any known problems, I "think" there was a recall of some sort on the '99, but you can check the main page here for any recalls for sure. There are also some guys on this board that own '99s and will be able to tell you a little more about it...
In case you do decide to jump aboard the green team, WELCOME!