The problem is that the racing is SO close, that really small things are the difference between 1st and 20th. As I'm sure all of us can relate, getting that last 0.01% is very expensive. So as long as there are people willing to spend the money to get that last hundredth, any team that doesn't will lose.
In the LAST race of 2008, which is the LAST race that those chassis will ever be used, McLaren spent $3mil and gained 0.1 sec. Ferrari was right up there with them, so they obviously spent the money to gain a similar advantage. But BMW, who was looking so strong early in the year, didn't look so good for the last half because they stopped development on the car to concentrate on next year's car.
Formula 1 is the ultimate expression of "Cubic Dollars." They can cut operating costs by regulating them, but they can't cut development costs because it'd be impossible to police.
It sucks that Honda pulled out, but they just weren't competitive. Only a few races in, Super Aguri Honda pulled out as well. It's just not a winning platform for F1, and with the economy as it is I definitely agree that they can't spend the money on development costs.
I don't know what they can do to clamp the costs of F1 without turning it into a spec series. Let's just hope the changes for '09 will make it more exciting for more people so attendance/viewership will go up