The following are my observations from running repair shops during that decade and should not be taken as apocalyptic. These are just my jaded comments. They're not as bad as I portray here.
Be prepared for nickels and dimes. I'm not sure if VW released patents on parts, but there were a very large proportion of parts that VW made so proprietary that you had to buy the VW part, and it was only available at dealers. An example: The crankcase vent tube. It uses a special squared off o-ring click connector that defies just replacing it with some parts store rubber hose, and it was $181 wholesale when I ran shops. To make matters worse, it's made of plastic corrugated tubing that doesn't play well with HC. Think like split-tube wire loom material without the split.
Timing belt changes are an absolute nightmare. To remove the front engine mount (right in the middle of the timing belt), you have to extract a 6" mount with 2" of clearance to the strut tower. It's a process of jacking the engine up, rotating the mount, lowering the engine, putting the mount in a little cavity beside the water pump housing.... it's intense. If you get the diesel, be sure to buy or make the special tool to hold the injector pump in place. Re-timing that pump isn't easy.
Buy a set of triple square sockets, but be prepared to shear off every bolt head the first time you try to pull a CV axle.
Changing the alternator (or A/C compressor, I forget) calls for removing the front bumper, which in those cars means both front fenders because they're all one piece. In reality, you don't need to. You can do it without stripping half the body, but it's not a fun job. Be prepared to strip and refinish about 30 interior pieces. They're painted with something akin to plasti-dip that turns into something stickier than a tabletop at IHOP after a flapjack festival, and the whole interior smells like you are melting a 64-box of Crayolas. It's seriously pretty oppressive.
Do not put in an aftermarket head unit unless you know what you're doing. It will set a CEL and turn your ALDL into a code-reader-killer depending on the reader. The BCM monitors everything from seat heaters to windshield washers, and yes, the radio. If you don't do a head unit properly with a special VAG COM harness, it starts sending 12v to a pin in the ALDL that is supposed to have something else. At the best you'll get a CEL with no comm to your scanner. At the worst, you'll get a fried scanner.
Re-clean all of your grounds for lighting, and don't use cheap bulbs. Unless the resistance of the bulbs is spot-on, it will tell you you have a brake light out. Usually "long life" bulbs are close enough, but a cheap, regular 3157 won't cut it. Grounds frequently get corroded which over-amps the socket. They melt and you sometimes have to get a new socket.
I would strongly suggest a manual. The 01A automatics in those beetles are disposable. Impossible to rebuild properly, and your only real hope is a big-dollar reman off the shelf, or getting lucky finding a used one that isn't wasted.
I do love me some ALH TDI. Sips fuel, decent torque, good aftermarket if you decide to turn it up to 11. I always loved the style. I think VW did a good job reviving the old Beetle. Aside from the problem areas (pretty typical for most German early-OBD2 cars), I think it could be a good bet. I mostly mention these above things to give you a jump start on what to expect. You may experience none of the above, but those are the common things we saw in the shop.
If so, I know where there's a good Maserati Biturbo for sale that you can use just in the rare case the Fiat is in the shop. 
