Right I'm sat in an Airport bored waiting for a delayed flight so I thought I would pass the time giving this a few facts and some context just in case anyone is still reading this!
First off lets be clear, obviously a 3.0 is going to cost more to run as a total package than a 2.0, there's no disputing that!
Lets take the 2 cars running costs over a year, a 2.0 which has the best fuel economy in the range and the pre face lift 3.0 which has the worst (M's excluded) and we will assume both cars never develop a mechanical fault and all figures (mpg/tax) are take from trader.
1) Insurance - its always going to be more for a 3.0 and than it will for a 2.0, could be a little, could be a lot and entirely depends on someones circumstances so we can't really quantify it here, nor can it be ignored.
2) Tax - The 2.0 is £240 and the 3.0 is £305 or about £5 a month, so not really a deal breaker by anyone's standards.
3) Servicing - Assuming one full service a year your talking a few extra litres of oil and a couple of plugs (and the labour to fit) for the 3.0 over the 2.0. Lets call it £50 and in reality the cars don't need plugs every service.
4) Tyres - Well if your running the same size wheels and tyres then there's not going to be a difference in cost. I know it can be argued that the more powerful car will wear tyres more quickly but in reality its just as dependent on your right foot.
5) Brakes - The 3.0 run bigger disc both front and rear but the cost of these over 2.0 from places like Brakes International for example is circa £5 per disc, again not a deal breaker and you certainly shouldn't need them every year anyway. Pads are basically the same price and fitting would be the same between the cars.
6) Fuel - this is the biggie really, assuming the 12k per year and using the quoted average mpg on trader the cars are about 6mpg apart which would run you to somewhere in the region of £400 or so depending on fuel prices where you are. Obviously this is very dependent on your right foot. This figure is equally true of a 2.2 or 2.5 as they delivery within about 1 mpg of the 3.0 manual. I can say from first hand experience with E46's this is true, but is still quite unbelievable when you think the 2.2 is nearly a litre smaller than 3.0! Auto's also delivery circa 1 mpg difference to their manual equivalent.
All in excluding insurance cost and no breakdowns/repairs a 3.0 going to run you to something like an extra £550 a year to run. Most of that's fuel and it assumes your changing the plugs/pads/discs every 12 months which your wouldn't/shouldn't be.
For a petrol 3.0 that's running 15-20 year old technology the E85 is pretty damn impressive on fuel and I can't believe anyone's complaining about it. What the hell were you expecting? Lots of owners report a typical circa 30 mpg which is roughly what I get. My old 2005 3.2 Boxster in comparison used to get about 23 mpg doing similar driving (Ok it had a little more grunt) and E46's I've owned in the past with 3.0 M54 engine used to get about the same as the Boxster probably due to the extra weight. For me even doing 12k pa an extra £50 a month would make the 3.0 more than worth it. Its got a better, more powerful, more reliable, smoother engine and is much better equipped from the factory in standard form, it gets bigger brakes, leather electric seats etc amongst other things and then tends to be optioned up much more than the 2.0's are. All this for the same sort of money as 2.0 these days, it does seems a bit of a no brainer unless insurance really is a killer or your doing mega mileage. Yes when the price difference between a 2.0 and a 3.0 was £5-10k then a 2.0 made alot of sense, especially new with a 3 year warranty for peace of mind, but now in today's market as a buyer I honestly can't see the appeal unless the financials of insurance/fuel that I mentioned are enough to steer you there and then if your unlucky enough to fall foul of one of the well document issues of the 2.0 then any saving you've made are probably gone up in smoke.
I'm really not trying to fall out with folks over this or upset them and its not "2.0 hate" for the sake of it, its just the facts of the case.