Is this a wize decision or should I run
I guess this is down to what you want from your bike, the 1000 is going to be heavier, use more fuel and be more expensive to tax and insure but it will be more capable of going very fast, touring and pillion work. The stock suspension does need work to get the best out of the bike, the OEM rear shock was under sprung at launch and unless serviced will be even worse with age, the front forks are adequate but benefit from stiffer springs. However a sorted Gen1 Fazer is an excellent all round bike and many that have moved away seeking pastures new have come back to the fold as nothing seems to do so much so well, I tended to chop and change bikes every 2-3 years (889 fireblade, 929 fireblade, ZX12-R, Speed Triple) but I have had my Gen1 for 7 years now and don't have any plans to move on for this reason.
What should I look out for and are high mileage bikes worth looking at?
I would rather take a higher mileage bike that has been well looked after than a lower mileage bike that shows signs of neglect. They can be susceptible to corrosion if neglected or used in all weathers the exhaust headers and bolts will be the best place to check for this. My favourite tip is to get the seller to evidence that they know where the exup valve is, that they can tell you what servicing it entails and how often they do this, if you get satisfactory answers then the chances are you have found a caring owner and a bike that's been well maintained. If they say they get their workshop to do the servicing then expect the exup valve to have remained untouched and potentially in need of seized bolts being drilled out and replaced. If you're looking at buying from a dealer ask if you can visually inspect the exup valve for evidence of it having been serviced and confirm for yourself that all the bolts (cover & housing) can be turned.
What are the big things that go wrong and are there major differences in the years?
The bikes are pretty bulletproof, it's only really the corrosion and exup that need to be kept on top of. There are no 'major' differences that should really be an issue, I do know that there was a slight change made to the carbs around 2003 but the chances are you will either buy a bike that has been 'ivanised' or will want to get this done at some point making an already moot point even mooter.
I do like to service my own bikes and is the 1000 a pleasure or beast to maintain?
As ghostbiker said once the AIS system has been removed servicing the bike is no issue for a halfway competent home mechanic, I wouldn't particularly class myself even at that level but as well as the obvious plugs / fluids / filters I have checked the valve clearances, rebuilt the forks, had the swing arm off, refurbished the brake callipers etc with no real headaches (the forks were a it of a pig).
Pat's site is an invaluable resource check it out if you have thee time & inclination, it has the main service items with guides on how to do these along with popular mods for the bike -
http://www.cartestsoftware.com/fz1/index.htmlPost back if you have any other questions.
Edit:\ Having just checked the for sale forum I notice that there is a very nice Gen1 up for sale