Ferry links - concept
Living in a watery place I really hope ferries will be a moddable thing in TF3. Arguably they are very niche, so I understand it not being a vanilla feature (although so are helicopters...)
Given the "miniature size" of the games, I don't really mean realistic ferries that need to wait to fill up and only then ship vehicles. What would fit the game-scale much better is ferries as a type of road:
Invisible in view, but logically no different to other roads. Thus private vehicles, trucks and busses can use it just fine, without much logical mumbojumbo. Visually, I imagine special ferry vehicles that need to be assigned on-top of such a "road", and depending on the length and number of ferries, that determines the speed of the "road". The ferries are the thing you visually see, just like other boats.
Granted, to make sense in terms of gameplay they would also need to fix a gripe I had with TF2: Bridges and Tunnels need to be much more expensive! It should always be the cheapest option to work with the landscape, by several multipliers, as it is irl. Then ferries become useful as a slow slow link for places where we just can't yet afford a bridge or tunnel.