I'm not sure where this goes since technically people could change this if they want, but it's about what's currently viewed as default, so I guess I'll put it here?
There are significant problems with how subs work in doubles+ matches. Most of these problems arise from subs mostly being designed around singles, but I also think it would be worth considering increasing the default substitution limit in doubles in general. My rationale for this is simple: in singles, you have 3 subs applied to one mon to deal with one pokemon's movepool. In doubles, each pokemon gets 3 subs, but you have two movepools to deal with. And while you could argue that the number of subs doubles (in that you now get 6 subs total), the fact that you have to split these subs as 3 to each pokemon means that's not effectively true, since any threats you want to sub for often need to be subbed for twice, once by each pokemon. In addition, sub eaters in doubles are much more common than sub eaters in singles, by virtue of the fact that the best strategy in doubles is usually to focus down one pokemon, meaning Protect goes from spending a bunch of EN to nullify a single action to an automatic +1 turn and therefore a mandatory sub for both pokemon in most cases.
This is in addition to the fact that sub rules are clearly designed for singles, which is made obvious when playing doubles. It is unclear with sub rules as written if "IF X is targeted by/under the effects of Protect" is a legal sub in doubles, which if it is not would make passed protect substantially harder to sub against, as well as necessitating spending 2 subs on any other sub-eaters that both opponents have. In addition, if you want to split the targets of your moves (which is admittedly rare unless you're trying to secure an A1 KO), the fact that "redirect to the other pokemon" is not a legal action clause and "your target is to use Protect" is also of questionable legality for the same reason "IF X is targeted by/under the effects of Protect" is (there is nothing in sub rules stating what makes an action clause legal or not with regard to specifying which pokemon is using the move in question) means you need even more subs just for Protect.
While it is sometimes possible for a single thing you want to sub for to be covered by one sub from a single mon, usually this is not the case, especially if it threatens both pokemon. Thus, limiting doubles to 3 subs per pokemon instead of more (I'm not sure if 4 or 5 would be more appropriate, I'd be inclined to test with 4 first and see how that works) leaves what can be done with subs much more limited than in singles. It is possible this is fixable by reviewing sub rules to make them more doubles-friendly instead of increasing the number of subs per pokemon, and ideally that would be the first solution tried, but that is also substantially more work than just increasing the default sub limit in doubles matches.