Co-op / Not so much game idea

I haven't played The Captain Is Dead, but one way to dis-incentivize a player trying to spring a Zombie Ambush is to significantly weaken the zombie's offensive abilities at first.

But only the offensive ability. You don't want to incentivize getting your friend killed just so you can immediately kill him or her a second time for the co-op win.

Actually, would the game end upon killing the player zombie, or just continue until the co-op team achieves a goal? On the flipside, it's plausible that more than one player character could turn zombie. Co-op goal for the zombies: convert all players.

Zombies, not vampires :)

If these were zombies raised by a lich or a necromancer, sure holy stuff would help. But most modern zombie movies (of which I have watched precisely zero) have some kind of science-y origin such as a virus or alien parasite.

The nice thing about science-y zombies is they can have whatever bizarre weakness you want them to. Hell, it could even be randomly drawn each game to force players to learn their traits. One game they are repelled by high-pitched sound, in another they get paralyzed by mild shocks, in a third they tend to lose limbs easily, etc.

To make players not want to become zombies you can carefully manipulate the power levels of each group throughout the game. The easiest to conceptualize this is as a graph. The x axis would represent time and the y axis represents power. The zombies power would start as a bell curve shape that levels into a flat line at what would be the apex of the bell. The humans power would be a two lines. The first human power line would start at the lower left corner of the graph, but slightly above the zombie power line (time=0, power=1) and goes towards what would be the apex of the bell curve. The second one would be the same as the zombies. The area before the intersection of the power lines would cover like 50-80% of length of the graph. This power level scheme or something similar should act to discourage players from purposely becoming zombies.

In fact, this power level scheme is intended to have several effects on game play. For the first 50-80% of the humans can defeat the zombie faction. The idea is that during the this time no-one will want to switch to the losing side. Of course you can't make it too easy either or players will get bored. You can also give them other things to do during this time. (Like gather items or fortify a base) Hopefully after this stage players will continue to want to be on the team. The stage when the zombie power is the same the human power would be the time where humans can potentially be changed into to zombies. This stage of the game would hopefully be really tense and the outcome is unknown. The zombie's power level may also have to go a little higher that the humans for a while so that they can make up for the imbalance in the first stage of the game. These effects based on this power level scheme should help you make the game you want.

To discourage players from becoming zombies you could have players have interesting abilities and/or items that they do not get to use if they are zombies. (We will say that zombies don't have enough dexterity to use fire arms)

Also to discourage players from becoming zombies you could some how make it risky to do so. Not really sure what the best way to do this is. The first thought is that players would loose a turn for zombifaction to take place and the humans could potentially win during that time. However, that would make for really lousy game play. Maybe that player would receive double damage on their next turn. Maybe they have all of the detriments of zombies and humans on their next turn. You could ask for additional suggestions as well.

Other thoughts:

If you want more zombicide and less story you can just give the humans abilities, items, fortifications and perhaps even a base and have them start killing zombies immediately. This would essentially skip to the humans and zombies have the same power stage.

At the start of the game zombies are NPCs. If someone get turns into zombie that means that zombies are doing fairly well. The zombified human player is probably a better strategos than a NPC, so now the zombies are at even more of an advantage. I sure you already have a plan to mitigate this.

Some thing that you may consider is that the humans could be waiting on a rescue party. As the rescue part gets closer they can also start killing zombies that they encounter. ( My original thoughts on this were that zombie power should be a bell curve. This would be a way to implement that) If the rescue party reaching the base would be the end of the game.

You could also build a game out of being the rescuers.

Also thought you could have a dose of an antidote that you could turn player back into a human. If you really like this idea the humans could alternatively use the dose of antidote to change a random zombie back to human and they would gain a companion that would grant the group some type of bonus. (This could work as a expansion or stretch goal also.) (It could also help with a single player mode.)

Items could simply have multiple uses on them, each with some set of requirements. For example (imagining stats running from 1 to 10)...

Laser Rifle
Shoot (STR 2+, DEX 4+): Does 6+DEX/2 damage up to range 8
Bludgeon (STR 5+): Does 1+STR melee damage
Start fire (DEX 2+): Spawn a fire token in any adjacent space
Salvage (INT 3+): Discard Laser Rifle and gain 1 Battery

You nudge the zombies into different choices by affecting their stats. Voice activated tech can make a choice uniquely available to humans, and immunity to radiation (or whatever) can make a choice uniquely available to zombies.