I'm not all that familiar with the 2000 5-series, I imagine they're good cars, so I'll just pass on a few personal musings, for whatever they're worth. First, if the present car is working just fine, why not just stay with it? The car would seem to have plenty of life in it, particularly in light of its being driven only 6000 miles/year, so proper care and maintenance should allow many more years with it. I'm not sure you'd see any overwhelming advantage, particularly in the fuel economy category if that is a conern for you, in getting the newer car. Maybe marginal improvement, but I don't think all that great.
If you do desire to have something newer, however, I think you're right to look at the 6-cylinder version rather than the V8. That makes sense if again fuel economy is a key concern. Also, I suspect that the inline 6 is a better, more reliable engine, and perhaps less costly to service.
Another bias, go with the manual transmission if you're of that ilk, again for fuel economy reasons, but also to avoid problems with the automatics.