you'll find that many people are biased... Gen 2 (2006+) owners tend to recommend the Gen 2, and Gen 1 (2001-2005) owners tend to recommend the Gen 1.
I've ridden both, and I've got to tell you that they are both very capable bikes. The Gen 2 leans more towards "sport" than touring, and the Gen 1 leans more towards "touring" than sport right out of the box. However, either bike will do either task just as well with a few modifications. My Gen 1 set up with top of the line suspension components and me on the seat will give a good competition to the average supersport rider on their full-on sportbike on any of my favorite roads. The Gen 2 can strap on some Givi Hard luggage, get a set of handlebar risers, and lowered footpegs to make it tour like a FJR-Lite.
It's really hard to say that one is "better" than the other, and the factors that make a person pick one over the other are normally personal.
For me, I prefer the look of the Gen 2. Hell, I don't think there's anything quite as sexy as the Gen 2 with the FZ1-N conversion done to it. However, I like working on my bike almost as much as I like riding it. Not to say that the bike NEEDS a lot of work, but for me, I have an easier time working on a carb'ed bike compared to a Fuel Injected bike. I don't like the complexities of the FI and computerized systems. For $10 I can have a hand full of jets, and spend an afternoon trying out different fueling scenarios....[< For an example of the extent of me being a Luddite, my perfect bike, could I build it right now, would be my big heavy steel FZ1 frame, with a Big Bang 09 R1 motor crammed into it, with carbs.>] You can also do the same with the Gen 2, but using a laptop and a Power Commander.
The Gen 1 has a slightly more relaxed seating position when compared to the Gen 2, but that's also subjective. On the Gen 2, the footpegs are slightly higher and the bars are lower from the factory. But, I have short legs and long arms, so I fit the Gen 2 surprisingly nicely in stock trim. In the meantime, in order to fit my Gen 1 comfortably, the pegs were a bit too far away, so I added Gilles Rearsets.
Typically, power delivery on a Fuel Injected bike is a bit crisper, but I drilled the slides on my Gen 1's carbs, and now the throttle response is amazing. I also advanced the timing, jetted it, modded the airbox and countless other fun things to get the power delivery exactly like I wanted it...
When it comes down to it, you can't go wrong with either bike... They're both very capable machines, but like anything else, both could use a little massaging to make it "yours" ... Some folks like one out of the box compared to the other out of the box... but let's be honest... who leaves their bike bone stock? Whether it's a pipe, or bars, or grips, or levers, or whatever... you'll change something to make the bike suit your needs.
So... I'd ask you several questions.
Are you more comfortable working on Carbs or on Fuel Injection?
How much are you willing to actually do to you bike? Will you do a pipe and grips and then just ride the wheels off of it?
If you're mechanically inclined, pick whichever one you're more comfortable working on. If you're not inclined to work on your own bike, and will take it to a dealer for every maintenance... just pick the one that fits you best and you like the looks of the most.
If at all possible, get a little seat time on each one.
Finally.. for what it's worth, since the Gen 1's are getting older, and they didn't really ever have that big of a following, aftermarket parts and accessories are starting to drop off a bit. Meanwhile, there are plenty of parts available for the Gen 2. But also think about the cost of the parts. A Power Commander is $300. A jet kit is $110 if you buy from a "tuner" or $30 if you use my method (which I've written up extensively). The 180/55 Gen 1 tires are cheaper than the stock 190/50 on the Gen 2, and most Gen 2 riders that like to ride a bit hard go with the even more expensive 190/55. Then, we have the amazing phenomenon of the Gen 1's holding their value better than the Gen 2's... You can almost buy a 2006 Gen 2 for the price of a 2003 Gen 1... Don't know exactly what's up with that... it's a bit crazy.
Richard, welcome to the forum. Welcome to the madness. If you have more questions, let us know. When it comes down to it, the decision is yours, but we can help you with questions that you might have along the way.
Members, let's all welcome Richard, and help him in his quest for Nirvana that is known as the FZ1.