There's no cost for the 16:9 if you shoot protected for that framing while composing for the framing you really want, however. How best to accomplish this multi-aspect acquisition is best determined by the DP based on the camera package because what's best with 1080P acquisition will not necessarily be the same for a 2.5K camera or a 4K camera.

Second, seriously evaluate the likelihood of certain distribution channels and keep in mind this is not a one-size-fits-all issue and it has nothing to do with theatrical presentation. Widescreen is not and hasn't been a limited to theatrical distribution issue going on more than twenty years now. Also, more and more the options for self-distribution are attractive for indies. Self distribution means you get to set your own rules (though it would be smart to protect yourself for future markets).

It's been a couple days that this thread has been dormant but several posts in here have been bothering me this whole time.

The linked article by the OP is wrong, for starters (besides it being obviously written by a non-creative toolbag), specifically with respect to Netflix. Netflix does not limit or demand 16:9 as the article implies. There is, however, evidence that many television stations might, for free TV and pay TV delivery. So, protect for TV and have that as an alternate version of the film for the lowest common denominator crowd and unsophisticated buyer whose money is still green and know that at the very least you can have your film seen as intended on DVD/BD and any DCP presentation (cast+crew, premiere, festival, etc.).

You're going to be delivering your film with many different audio streams separate from the video so making an alternate video stream (assuming you've shot protected for 16:9) is just another part of your deliverables package. This won't even be close to the most tedious part of delivering a film for distribution.

So, make the film you want to make. Shoot it composed for the aspect ratio that serves the way you want to tell the story (though making sure your DP is on board and you two are in full agreement is key). There is often a sentiment expressed in almost any discussion of aspect ratios that somehow certain genres don't warrant certain aspect ratios or somehow widescreen isn't appropriate for certain kinds of films. That's bullshit. That's worse than conventional thinking, that's flat earth thinking. Don't be controlled by fear and ignorance. You can have your cake and eat it too, if you're clever and careful.

@matt_gh2 Yes, that's the scene where HAL reads their lips.

Kubrick and George Lucas exercised more or less full control over how their films were exhibited in theaters. Others may have been less fortunate, with their films projected with a 40W light bulb and tin can speakers!

Netflix does not crop ( not!) http://www.theverge.com/2013/7/18/4534160/netflix-cropping-movies-streaming

HAL 9000: I'm sorry Dave. No matter what aspect ratio I choose. They always crop it to death on basic cable!

LEFT Cinerama ....... RIGHT: Basic Cable Crop

Unless there is a great reason to shoot 2.35/2.40, I would shoot 1.85 protected for 16:9. (You set up your framing for 1.85 but actually shoot onto 16:9, planning to remove the additional vertical lines in post. However, you protect your 16:9 frame so that you can distribute it this way as well for video.)

Odds are, most people are going to see your film on video somewhere, not in a movie theater.

"This sounds obvious, but sometimes let’s say you shoot CinemaScope anamorphic with 2.35:1, you have to go much further back to go to a wide shot, in terms of height. Otherwise, you shoot medium and close-up all the time. If you don’t scout out your location, it can be really bad." Darius Khondji

Unfortunately, for home video distribution the article is closer to correct than not. If you want to be safe you'll want a clean 16:9 version of your film. Having a letterboxed film won't prevent it from being sold, but odds are you will have someone else down the line, without your knowledge or input or any oversight, crop out a 16:9 version from your film that you might not be terribly happy with.

On BD, there's nothing stopping letterboxing. It's still most common for truly widescreen films to maintain their proper aspect ratio in that form. Not so on TV or streaming. Just take The Dark Knight Rises for instance. It was mostly shot anamorphic 35 and in the BD release you see the narrative portions in a 2.40:1 letterbox and when the 65mm action scenes come up the screen expands to fill the full 16:9. Watch it on HBO or streaming and it's 16:9 all the time, with the anamorphic portions either center-cropped or pan-n-scan.

Remember that feeling when TVs got wider, even at your parents' house, and the whole "letterbox herrecy" thing was going to be a thing of the past because we were finally getting rid of NTSC and all such lowest common denominator considerations for all the less sophisticated people consuming media in the world? Yeah, well, they didn't go anywhere and all those jackoff video engineers in QC and broadcast departments all kept their jobs so they could go on leaving their mark on new formats and new technology for all the Joe Six Packs out there, so they wouldn't have to ever ask "why isn't the picture filling my screen?"

edit: You could take a page from Super 35 and shoot what's called "common topline", where rather than compose with a 2.40:1 window in the middle of the 16:9 frame you shift this thinking up so that you're composing with a 2.40:1 window at top of frame. Then you have a somewhat sloppy looking 16:9 version with lots of bellies framed in mediums and MCUs that are now medium shots but, hey, it's good enough for James Cameron. This let's you exhibit and enjoy a 2.40:1 extraction from the top of this frame and perhaps you can urge that this be the version for BD release letting streaming or television buyers use the 16:9 version if need be. These will often be totally different buyers for every region that you sell, or that your sales rep sells.

2.40 is typically a "big" movie format, usually used for films that have a large scale (like epic adventure films and sci-fi flicks). 1.85 is a more traditional format used for films that are more intimate. So if your comedy is more on the smaller scale of things (like nearly all comedies), then something like 1.85 would be more suitable. If you are shooting a large scale comedy (think Ghostbusters) then 2.40 would be a more suitable format. Hope that helps with your decision. 16:9 I would reserve for web content or TV shows.

If you ask me, use 16:9 and concentrate on content.