Overall, the 97-99 may be the "worst" to buy but I think you have to ask why you want the car. If it's going to be a daily driver and you're going to sink almost every last dollar into the car to get it, then you're better off getting the latest greatest Boxster. On the other hand, if it's going to be a fun car, you enjoy turning a wrench every once in awhile and if something mechanically catastrophic happened where you might be PO'd but could survive it, then there is nothing wrong with looking at '97-'99. Many Boxster owners don't drive more than 5000 miles a year and you can get a pretty nice car for $15k to $20k. Make sure you get a Porsche Pre-Purchase Inspection. I didn't but I recently got a Porsche Post-Purschase Inspection
and the mechanic thought it looked great for a '98.
The killer defects - porous blocks and slipped sleeves are gone by now unless you it happens to be a garage queen. As I see it, it seems like RMS and intermediate shaft failure is pretty much across all model years (same M96 engine.) I view Boxsters with factory replaced engines as a postive since the remanufactured engines are built to tighter specs.
One good thing about the older Boxster is that a lot is known about common failures and many are repairable by the DIYer; convertible top cables and alignment, air/oil separator, ignition switch, assorted microswitches, clogged drains, motor mounts, airbag light, coolant tank, window regulators, MAF and 02 sensors. A lot of basic maintenance isn't so bad; brakes, cabin and air filters, throttle body cleaning, coolant, radiator cleaning, oil change. The shortcoming of having a plastic rear window is somewhat address by third party glass window top suppliers (one manufacturer says that they are working towards providing a DIY DVD and still not counting out Tool Pants in creating one.)
The early Boxsters have taken most of their depreciation at this point and with the advent of Spec Boxster racing, it may slow it down even more. The early Boxster can be a great hobby car (albeit an expensive one.) With a lower investment into it, you stand a better chance of realizing your daydream of putting a 3.4l engine into it someday (snap - that's my daydream.)
Different strokes for different folks.