Personally, I 100% agree with the OP. The battles being allowed to drag on for hours is really hurting the impact of this new activity. (And as a long time player of Sea of Thieves, I think this activity is hitting a lot of things right! Good action, lore, and on demand pvp is a good way to liven the game back up. There are just a few things diminishing the strength of Hourglass battles.)
Here's why it's bad to let battles go on:
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It dilutes the matchmaking. If everybody in your skill range is constantly locked in never ending battles, then you get to sit in ridiculously long queue times until one of them ends their fight. Then there's a delay between the end of their fight and them resupplying and getting back into the fray. It slows the experience down for EVERYONE not just the people trapped in age-long fights. No queue should give you enough time to shower and make a sandwich before you find a match (and yes, I have literally done so).
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Most players don't want to be trapped in a single engagement of cat and mouse forever. If both crews go in with hundreds of cannonballs and planks, then the fight of attrition will be nigh inexhaustible. Sure you COULD use a crazy strategy and hope it pays off (i.e. ram keg) to try and end the fight, but the vast majority of crews aren't going to do something like that until their supplies are depleted and it becomes a necessary course of action. Something needs to be done to shorten these engagements to a reasonable time frame.
The idea of shrinking the combat area is a good one. I'd even suggest shrinking the initial area by 25-30% already in the case of sloops. Too much area to run around and avoid combat when the purpose is to ENGAGE in combat is counterproductive to the flow of the gamemode.
I like the idea of "powerup" barrels but I don't know if it's reasonable to add. It might be cool for a Phantom ship from each faction to join the fray every 10 minutes or so to bring said boosted supplies, but I won't put a lot of faith in that option until we hear how plausible it is.
Putting a cap on supplies doesn't really seem fair either, because it removes any element if preparation from the mix. Especially since this is an open world engagement, time spent preparing in said space should be an important factor in the battle. So curtailing supplies doesn't really seem like an acceptable solution to the issue.
What I really think needs to happen is a strong time limit be enforced. If the invader can't defeat their target in 20-30 minutes, the game should strike a draw and return the invader to matchmaking/a new instance. You don't get a win or loss if that happens, which incentivizes both crews to be more aggressive if they want that kill credit. Sure, nobody wants to spend 20 minutes in a fight for no return. But when the other side of the coin is spending 2 hours in a fight to gain one notch on your streak or lose everything and quit playing the game then and there... I think most of us can agree the first option is better.