I have both, The 2001 E39 530d Auto with 271000kms and the 2006 E60 530d Auto with 64000kms.
The E60 does NOT compare to the E39 when it somes to comfort and suspension.
Niggly bits about the E60 that I dislike:- iDrive Freeze, ECU override of gear changes (supposedly for a smoother change), fiddly electronics, not being able to switch the radio off completely, ultra lightweight panels, silly spacesaver wheel(which does not fit my car - I have the M5 disc and wheel setup), lack of a temperature gauge proper and the most irritating is the seatbelt warning gong.
Although my E60 has M57D30TU2 coupled to a 6 speed Auto, I tend to get better consumption from my E39 on mixed driving.
The E39 power/torque delivery is its downside, when compared to the E60 - The power and torque rush is phenomenal.
For rapid motoring on freeways with exceptional open road economy, I'd use the E60. For daily driving of both highway/city, I'd use my E39. The only downside of this are the pr!cks that do not know how to open a door without denting the car next to them.
In 271 000kms, I have fitted 3 Turbos, 1 waterpump, 2 belt sets, 1 set of coolant hoses - ZERO gearbox issues (just a stiff link cable), 1 set of shocks (front and rear), 5 sets of tyres, 1 windscreen, 2 window mechs (LR and RF), 1 set of Angel eye globes, 1 set of injectors, 1 set of rail pressure sensors, 1 x Airflow Meter, 1 x Pre Feed Fuel Pump
I am not even going to go down the road of the E60................:bangdesk: