I think the swimming animation already exists but not exactly sure what you mean. I'm assuming you mean in first person? I love the train idea but how would that work entirely? I think it would really be useful to get you to certain areas and you would still need your vehicles to get to other areas outside of the train "loop". Fishing seems like a no brainer, would open up for a new variety of cooking benefits since you still need to hunt other land animals for food, besides, all the bodies of water available in the game would make those areas even more vital. Boss Zombies makes sense since there are huge labs in the game that would call for them.
Just my opinion but animal traps might not be so necessary since they're easy to hunt, dual-wielding would be cool but I dunno how well it could be implemented unless there would be some way to combine the weapon choices so it only takes up 1 slot on your belt for easy access, if not, you'd have to constantly confirm if you want to dual-wield or not for small arms. (Definitely deserves some dev discussion though). Swords are cool but who knows if they would be something that majority of people would use, since, lets be honest, most people just like to Pew Pew anyway.