We should remember a few things about timeline theorizing in general.

There are two ways of doing it: Using Personal Opinions, and being Unbiased.

An Example

If the developers say, for example, OoT is the IW, then there will be people who agree with them despite the inconsistencies, and there will be people who disagree with them because of the inconsistencies (based on unbiased info). The reasoning behind those who agree with them is "What the developers say, goes. Inconsistencies are not a problem, they are bound to happen". The reasoning behind those who disagree with them is, well the obvious, "They're just wrong, there is contradictory info from the games." I have to remind you that there may be indisputable inconsistencies with OoT being the IW found in both the SNES and GBA versions of ALTTP.

I feel that another reason can be made for those who disagree: If the developers say OoT is the IW, yet there are inconsistencies, then what's to stop anyone's personal opinion theory that has inconsistencies from being canon as well? Whether they are aware of the problems is irrelevant unless they acknowledge it in the future (if they haven't done so already). The games stay the same for all of these years, but people can change their minds whenever they want. They should not receive any blame for the problems, nor should they be inclined to remake a game to fix it.

The Outline

With that being said, even if there is conclusive evidence that goes against someone's theory, that person can still use his personal opinion and say it is canon. There is nothing wrong with that because Timeline Theorizing can just be a Hobby that has no affect on the real world to some people. Zelda theories, stories, timelines, are information in Fiction. This fiction is not going to affect every theorizer in real life outside of zelda.

So we can theorize however we want, but I suggest we inform others just why our theory is what it is, a personal opinion or an unbiased piece of info, instead of passing it off as fact, and I suggest the reader to acknowledge it and not unnecessarily discuss anything about the theorizer him/herself.

This also means anyone can believe in linearism, splittism, 3, 4, a million timelines, a preference of an english version over the japanese, ignoring developers intent, ignoring official artwork, anything they want. When the developers unveil the timeline and cover everything that they feel needs to be covered, we can look at it however we want.

I think a change is needed for those who theorize otherwise, myself included. I believe this is the best guideline for any theorizing, no matter what it is about.

NOTE: This is not meant to replace the current guide, but to simply add to it. If you have any additional input to what theorizing should be, feel free to mention it.