I'm going to start off with the full disclosure. I am currently editor of a 3D film, and have previously worked on both motion capture and stereoscopic live-action 3D films. Also, I firmly believe post-conversion is terrible and is the number one thing the industry is doing to harm the advancement of 3D. Both live action 3D films I've been involved with have been shot completely stereoscopically in true 3D.
I don't believe that directors are particularly wise to resist the move to 3D. There are a lot of benefits to shooting in 3D and to embrace the technology will allow filmmakers to be at the forefront and to dictate the advancements in the technologies - rather than having the producers dictate the advancement of the technology.
It's just like the move from black & white to colour, from mono to stereo to surround, etc. 3D is going to consume a large portion of the market share in the coming years. Also, working with 3D isn't really that much trouble. You have to be smarter with your metadata and think a bit more about what you're doing ahead of time, but that holds true with any profession as technology becomes more complicated and more capable.
People will expect more out of your product. Most people now expect cars to have airbags, ABS, air conditioning, and power locks and windows. As technology advances, people will expect new filmmaking technologies like 3D to come "standard". Will it increase the cost of films? Sure. Will ticket prices rise? Definitely. Do cars cost more now than they did 15 years ago? Absolutely. Has the experience of driving improved? I would argue that it has.