Welcome to the forum.
1) You question is an age-old debate that wages multiple times per month across many forums. Do a search on this and other forums on the topic and study the many hits you will get for additional insights to what you'll get here.
2) Whether the 540 or the 528 is the best choice for you is a very personal choice, and none of us can make that choice for you. So I HIGHLY recommend you test drive as many 540s and 528s as you can find - look at local BMW dealers and used car lots. Yeah, you may not be interested in or maybe cannot afford their particular car, but don't tell THEM that.
3) Your preferences expressed so far indicate to me that a BMW 5-er may not be the best car for you. You sound better suited to an Accord V6, G35, Lexus ES 300/330, or Acura TL. All are fine autos. However, if you absolutely MUST have rear-wheel-drive, then I think the 528 automatic will suit you fine. I test drove a 2000 528 5-speed and my overriding impression was how much more enjoyable the car would be with the automatic because the 5-speed felt like a lot of work for very little reward. In fact, maybe the 2001+ 530i would be a great choice.
That said, let me share how I feel about the subject, after a few test drives of 528s and 540s and talking to friends who owned both: The advantage in nimbleness & handling offered by the 528 was IMHO very subtle, whereas the 540's advantage in acceleration was MUCH more dramatic. Also, the 540 offered a few items as standard equipment (dual-zone climate control, etc. - varies by year) that were optional on the 528.
Reliability: The cold hard fact is that no E39 BMW will be as economical to maintain as the other marques mentioned above. I hate to admit it, but based on my friends' input as well as hanging in multiple forums since 10/2004 I've concluded that the I-6 has an edge on the 540 in terms of cost to maintain, especially a "normal" 528/530 compared to the 540 Sport Package, mostly because of tire wear and replacement.
for common problems and fixes of the 540. That list indicated which issues are common to the 6-cyl models. My personal finding is that I've spent about $1500 to $2000 each year (annualized) for my car's maintenance and repair costs, and I provide all of my own labor.
On that note: BMW parts are not hideously expensive (check out Porsche and M-B costs some time), but labor is high, so if you own one of these babies, you need to be prepared to turn a wrench or two.