I don't agree with giving less repair kits to smaller ships would be fair, I think it would shrink the battle time a lot and give an unfair advantage to larger ships in the open world. Three repair kits are fine by me (perhaps give a couple more to the smaller ships when they enter the open world), when your armor drops at 1/3 you can use two and be up and running again plus having one to spare for other repairs gives you some peace of mind.
What I'd like to see so far is two things:
Give the repairs a flat 0% in time required to finish them when in Sail stance, -10% time when in Gunnery stance and 15% (perhaps 20% ?!) increased speed when in Survival stance with an additional 2%-5% increased effectiveness of the repair.(eg: if one repair repairs 100 HP, in Survival you get 102 - 105 HP)
Been able to chose what type of repair supplies you want. For example you want more wooden planks/metal sheets, tar and rope to patch holes or you want more cloth and ropes for your sails. That would affect the effectiveness of the repair.