Both will be relatively reliable. Both will get good fuel economy. Some MKIVs seem to do better at highway mileage than the MKIIIs because of the different turbo design, and different aerodynamics.
Both generations have their issues as well. The MKIII power windows tend to fail, and it costs about $150-$200 for the part assuming you are willing to rip into your door and fix the problem yourself. (of course you can avoid this by going to manual windows) I am not saying it WILL happen, but it can. I have a 98 with power windows and have not had to replace a regulator. I have had to rebuild the steel cable which runs the system. ($10 vs $180) Windows-wise, the MKIV have a plastic clip holding the windows up. These can snap leaving you with an open window until you can get to a dealership. This is covered under an extended warranty, though.
The MKIII has a more traditional style wastegate turbo. The MKIV has a VNT turbo. The VNT will give smoother acceleration, and has to push less when cruising on the highway. If you are looking into modding the car, the VNT CAN be more prone to breaking. Precautions can be taken, but it's not always perfect.
Overall, they are both very good choices. The MKIIIs are available only in 5-speed while the MKIVs have the automatic tranny as an option. If you plan to do your own oil changes, the MKIV is much easier to do if you buy yourself an oil extraction vac pump. Don't have to jack the car up at all. You can just suck the oil out of the dipstick...and the filter is right there on top.
There are a few discussions on here in the past, so I suggest searching through and reading up. Last point to mention, the MKIII is a lighter car, and feels a little more nimble, but the MKIV has a smoother ride, and a more 'luxury feel' interior.