As far as I see it, when it comes to passive abilities such as Bleach's intangibility or JoJo's Stand invisibility, then they should be negated/equalized for VS thread purposes. By not doing this, you eliminate more than half of the potential matches that can be made for any "character A" simply because "character B" who they are fighting doesn't have the same mechanics in his verse that allow harm to come to character A in character A's verse.
When it comes to simple verse energy equalization, like Dragonball Ki and Naruto Chakra, there is really no conflict involved. But of course, there are the afforementioned "I have 'X' powersource, and you don't, therefore, you can't harm me in any way" cases. To mitigate this problem, equalization is necessary and can be easily applied, otherwise there is no purpose of the VS thread one would try to make in that regard.
However, when it comes to things like Fate Servants who are immune to "conventional weapons," I believe that goes beyond the equaliztion discussion and into a "hax or NLF" discussion, and should be handled separately. The same goes for "Character A can only be killed by this specific weapon which only exists in character A's verse and only one guy from character A's verse posseses it", in which case, either a VS thread should probably not be made for such a character, or a thread can be made under the premise that they can kill character A without the specific weapon, but it would not be added as a legitimate match to either characters page because the rule was bypassed.
As I see it, this presents 2 solutions:
1. We make an official page detailing the equalization rules for each verse that can't be conveniently equalized due to some rogue element in their series that would make a VS thread one sided.
or
2. The equalization rules are made on a thread-by-thread basis, and are determined by either the thread creator, or the debaters in the thread.
The issue with the first solution is that it would be quite time consuming to go through every verse to see if they have a rogue element that makes a VS match inherently unfare. BUUUUUUT, this can be avoided by doing it over time instead by having all of the staff memebers with reasonable knowledge of certain verses point out the ones they know to be problematic, and can simply add new rules to the page as the issues arise. Eventually, mostly everything will get covered.
The issue with the second reason is that many VS thread makers can be subject to bias, which in turn invites unfair match conditions by not properly applying verse equalization to the right characters, and leaving it to the debaters would likely derail every thread by arguing about equalization instead of the match in question.
So you guys decide! <3 But I'm sure someone will come up with a better idea than me.