I think I read an interview of Nolan where he said that if he ever makes a 3D movie it would probably be in converted 2D, because A: he can shoot scenes the way he always do (well, with 3D in mind, of course) and B: because he could better control the 3D effect during the convertion.
Usualy as an audience I prefer the thought of watching "real 3D" over "converted 2D" (and most of the time the effect IS indeed better), but from a filmaker point of view, converted 2D have some advantages that are debatable. And yes, even older movies like Jurassic Parc and Titanic got some impressive 3D convertion.
My only "problem" with 3D is the depth of field / camera focus effect. In a 3D movie the audience should focus on what they want. There should not be depth of field at all. For exemple it just looks weird when your eyes focus on something on the foreground that is all blurry. Depth of field is already a way to "simulate" 3D on movies since the beginning of cinema... So adding 3D to depth of field makes the job twice, in a way. But of course it's something that the filmakers are not okay to drop, because it's a tool to lead the eyes of the audience, it's part of the director's job AND they should also make a second version of the movie WITH depth of field for the 2D release...!
About the 3D during dark scenes: to me it really depends if you are in a theater with passive glasses or active glasses. Most of the time I found that active glasses makes the movie even more dark. I prefer passive glasses in theater (the ones that you buy once and keep with you and use again next time) I rarely found the movie too dark with them. BUT on a 3DTV, where you can choose between several lighting options, the active 3D looks much better than passive that is half the definition of active 3D, so it's not really "full HD" (even if passive 3D is usualy easier for the eyes on most people.) Anyway... that's why even if I like 3D I totaly understand people who just want to watch the fucking movie without bothering about all those technical possible troubles!