Now that would certainly not work. So consider this scenario in round 13 with two teams left.
Team A = 117 cards
Team B = 30 cards
Team A can field 3 legal deck and team B can only field 1. If team B wins 1 match they would then win the whole war since Team A would lose 78 cards and only have 29 left. For a event that long no way you should have a huge advantage like that and lose in 1 match.
Ok, let's actually look at a few scenarios.
Scenario 1, 500 card vault, team goes 7-2 or approximately that ratio until the end:
500 7-2
round, vault changes, # players in the round, record for the round
1 500+42-12=530 9 7-2
2 530+42-24=548 9 7-2
3 548+42-36=556 9 7-2
4 548+42-48=550 9 7-2
5 550+42-60=532 9 7-2
6 532+42-72=502 9 7-2
7 502+42-84=460 9 7-2
8 460+42-96=406 9 7-2
9 406+42-108=340 9 7-2
10 340+42-120=262 9 7-2
11 262+36-132=166 9 7-2
12 166+24-72=118 5 4-1
13 118+12-78=52 3 2-1
14 52+0-84=0 1 0-1
Scenario 2, 500 card vault, team goes 5-4 or approximately that ratio until the end:
500 5-4
round, vault changes, # players in the round, record for the round
1 500+30-24=506 9 5-4
2 506+30-48=488 9 5-4
3 488+30-72=446 9 5-4
4 446+30-96=380 9 5-4
5 380+30-120=270 9 5-4
6 270+30-144=156 9 5-4
7 156+18-84=90 5 3-2
8 90+12-48=54 3 2-1
9 54+0-56=0 1 0-1
Scenario 3, 500 card vault, team goes 2-7 or approximately that ratio until the end:
500 2-7
round, vault changes, # players in the round, record for the round
1 500+12-42=470 9 2-7
2 470+12-84=398 9 2-7
3 398+12-126=284 9 2-7
4 284+12-168=128 9 2-7
5 128+6-90=44 4 1-3
6 44+0-36=8 1 0-1
* note - while this looks harsh, it's exactly the same as the current rules until the cap is breached in round 6
It should be fairly likely for the war to be over by round 13 or before. What you will notice in the above, is the majority of the war involves a majority of the players. The rounds on the end where the team's vault is destroyed and they're playing with only a few players tend to be brief, win or lose. The war is unlikely to go beyond 3 months (12 rounds).
Regardless, let's walk through your particular example. Other teams would be long gone by round 13 anyway.
In order for team B to have 30 cards in round 13, they must've had 90 cards the prior round and 3 players and won twice(+12), and lost once(-72). You will note, that by above schedules, team B required a record of just slightly less than 7-2 every round up to round 12 to have a vault with 90 cards left in it in round 12.
Even in this case, team B must've dropped to 1 player from 3 in round 12, how is much different than team A dropping from 3 players to slightly under one (29 cards) in round 13? The difference in performance between the two teams in the 12 rounds leading up to that point could be just 1 extra loss for team B in round 11 or close to it. Either I don't see your point, or perhaps I don't agree that it's important. These teams have both had amazing, nearly identical records to reach round 12 with those vault sizes.
And the point is to wrap up the war sooner, which is exactly what this does. It seems worse to me to wait 3 weeks in real time for Team B to win 3 times in a row to take a victory. 104 players long gone, 2 on standby, and the last 2 guys battling for nearly an additional month by themselves. Not to mention the extra rounds before that point.
I guess I find the more valuable part of the war the part where there are more than 2 people participating in it. A schedule like the above wraps up the finishing rounds when there are less people quicker, making them higher stakes.