This is a limitation, or rather a leftover feature from RCT, of the engine. I don't know if it's deliberate or not.*) Make water flow in holes lower than the surrounding water level. These holes should obviously flood.
OK, over to my wishes ^_^
Be warned, some may already have been mentioned, with slight variation and/or different wording. Also, this was intended and written as a letter to CS himself, so keep that in mind if you think my wording seems strange at times.
Expectations for the first patch:
The AI should also stop building some of the most ridiculous track combinations. Preferrably, make them build straighter routes. And have them reuse roads, so that we can avoid having three or more roads running next to each other.
An indication of the expected life of industries, or earlier warning of closure (i.e. 3 months), and/or reduce chance of closure.
When building tracks, if a new piece will destroy a building, highlight that building in red. This makes it much easier to avoid accidents while building through a town. And/or display warning. Make toggleable.
An option to (temporarily) disable building/scenery removal. It's really annoying when I want to extend an underground station, but end up demolishing half the town while trying to right-click the end of the track. Maybe you can make it so that underground mode limits interaction to underground pieces. A work-around today is to use shift to place a new track piece underground, but that only works if the station happens to be on the same level.
Optimisation: When I use Underground view combined with Hide foreground buildings, the buildings disappear rather than become transparent. However, judging by the decrease in performance, the game still draws the buildings.
Make user-made scenarios stand out from the standard ones, i.e. different color.
Wishes for the first patch:
The ability to buy land for exclusive use, and buying exclusive transport rights and the likes in towns. Like in the old Transport Tycoon. Or at least give an explanation to why it wasn't included.
Company take-overs, like in the old TTD.
The ability to duplicate a train. I often make long, two-way railroad tracks, sometimes with multiple loading stations, and to keep the ratings high, I make many medium- to long-size trans rather than one or a few gigantic ones.
Alternate editing modes: Click and drag for long segments, or at least click and hold the build button for rapid construction.
Train servicing, or at least longer lasting trains.
Wishes for the first expansion pack:
Larger maps! Atleast double the size, preferrably quadruple it (i.e. double width and length.) Also, make generated landscapes look more natural.
The ability to shape airports. I.e more runways.
Endless Games: On the main menu you have the option to make a new game with the ability to set game options or let the game randomly decide, with the ability to save presets. I know this can be accomplished in the scenario editor, but it's kind of a hazzle. At least make the addition of a "Custom Scenarios" tab on the New Game menu.
This one should actually be implemented ASAP, preferrably in the first patch, but judging by the amount of necessary changes (graphics, balancing all the attributes,), it would probably not be justifiable for anything but an addon pack. What I'm talking about is more wagons. We have all these locomotives that do speeds well above 100 km/h, but the wagons only do 80, until much later in the game. Also, more non-train vehicles.
Make multiplayer, not just two-player. This is what I wish for the most. And then comes larger maps.
Graphics idea: Cloud shadows passing over the map, and weather effects. Although it's quite unneccessary ^_^