I sort of like guy_fawkes' idea. I don't think the "abuse" potential would really be all that big a deal since it comes from own element.
If you knew earth could field 8 graboid decks instead of just 4 would you really ignore the possibility they might use them against your team? Even if we have 8 matchups and 4 graboid decks, all 8 opponents need to consider facing it. It's not like it's a random thing out of the blue that wasn't on their radar. If it features strongly in lots of the decks we want, odds are we started with a lot of them as it is.
And anyway, a lot of successful decks are ones with off element components, precisely because it makes more sense for opponents to prepare to handle on-element threats than off-element ones, even if they know the option exists. Those are still limited.
Take an example from darkness. How many devourer decks will you field before people get wise to it? Is that abuse, or is that just part of the danger of fighting darkness and something teams should have to always respect as an element specific option? If you field 9 devourer decks in round one, then find some completely new darkness terror to field across the board in round 2, is that abuse, or the dangers of fighting elemental masters that happen to have those options? In some ways, the always-a-threat option is just elemental flavor. Why should some teams worry almost as much about devourer decks from earth as they do from darkness anyway? If darkness happens to lose all 4 of it's inital devourer decks, should other teams stomp through the next round knowing the masters of darkness can't produce a devourer? I'm not sure a set of bad matchups should remove elemental strengths like that.
The only thing the war would lose is the ability to predict when elements ran out of specific own-element cards. Early on, that would only point to cards they didn't want enough to bring anyway. For the first 4 rounds you'd never be sure what got discarded. For round 6+ it would affect that. Is that a huge deal? In some ways I like that part because it gives vault tracking more prominence, in other ways I dislike it, because wars based on attritional attributes like that have a sort of monopoly-type ending phase to them. The losing player knows they're dead half an hour before it actually happens and they play through bleeding out until they're finally bankrupted. The game is really over at the 2/3 point in all but name. You'd still benefit from tracking off element vault options, but you could never rule anything out within element.
His idea does allow elements to adapt somewhat after it becomes clear what deck ideas you brought are suitable and which aren't. For example, you could see elements like gravity decide to turn every discord deck they beat into another discord/blackhole deck. Or maybe something brand new pops up when they get an interesting salvage. In some ways that's a bit annoying, in other ways it means you can't ignore the strengths of an element mid-war because they happened not to load up on huge stockpiles of blackholes or something before initial contact. If in round 3 a team only has one deck that works, expect to see a lot of it rather than just watching them die. It also helps teams take better advantage of salvage. Maybe gravity takes the discords precisely because they can swap in new blackholes to go with it. Maybe time only takes momentum salvages because they can swap in dune scorps. Maybe darkness pulls out a voodoo deck when it wins a set of gravity pulls. I think one result is the weakest decks from the first rounds probably get swapped to something new. Meaning elements remain dangerous more based on their creativity and adaptability rather than their initial vault guesses. You ability to predict upcoming decks from opponents has as much to do with their salvage opportunities as vault tracking.
You'd also probably see more usage of on-element nymphs or cards that are only good upped (think antlions).
I could go either way with guy_fawkes idea or some variant of it. I like the way it is now, but I also like the increased elemental danger/flavor and adaptability his idea suggests.