In my experience the difference in running costs between a sensible 3 series and 5 series (even as Sport or M-Sport, but as distinct from M's) is marginal . I can't say specifically on the e90/e60 comparison because my 5's have been e39 and f10 and our e91 is a 4cyl but in comparing e36, e39, e46, etc. in a variety of 6cylinder examples its pretty much swings and roundabouts.

The costs might be for slightly different things (e.g. I don't think we've had to change a bushing, balljoint, wishbone, etc. on the e91 - and by inference e90, but its had a couple of small issues that haven't occurred on other models and on the e39 something of the list of bushings, etc. would have been std wear and tear items over the years and miles).

As regards reliability, I've never been left on the road by a BMW and only once had a failure to start (a flooding issue in an m52 e39, my own fault) in well over half a million miles of BMW motoring.