The water with some blocks looks like a solid block; the water doesn't cover blocks (slabs, stairs...) and looks bad. Only the 'Item frame' block is covered by water and looks good.
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This is a design choice. Every block in the game have an ID, and water, lava, etc are blocks too.
You can't have a block with 2 IDs, to "fix" this would require to create an ID for every water/block combination possible.
EDIT: Paitings works like item frames, and they are not blocks, like Ezekiel said.
Couldn't there simply be a damage value to indicate whether or not the item is submerged? Though I suppose there's an issue with varying water levels (as you get further from the source block). But still, making blocks entirely underwater contain water like that dock in the picture would go miles for making the game look really nice.
I still disagree. In your example, you explain how water once worked as it was intended to, but that doesn't mean that after fences were made it wasn't behaving in unintentional ways. What happened was that when fences were added there was two methods to deal with its interaction with water at that time. 1, Fence gets destroyed by water; 2, fences hold back water. #2 was the lesser of 2 evils.
I'll draw your attention again to the top of the page. "Won't fix" does not mean "Nothing's broken" it means "We realize something is broken, but we aren't going to fix it for various reasons." I think its okay that Mojang to chose this. But I also think its okay that some people wish Mojang would find a way to around Minecraft's technical limitation. Perhaps, for example, finding a way to add clipping(collision) to entities that prevents player/mob movement but not water.(and then making fences and such into entities instead of blocks)
edit: changed some pronouns to be more specific, but I'm not clear on what was confusing. (I have that problem sometimes with my writing)
I think the way to solve this issue is to graphically put water in over the items that should be submerged, such that the item 'Block' still exists, but appears to be submerged. This would make for some odd phenomenon, however, which would be unfortunately difficult to fix, such as water actually being air where a sign block is placed, and water not flowing further. The way to fix this, I guess, would be to include a part in the game where if a 'graphical water' has an empty space to any side(except up) open, it will place a non source water flow.
Oh, and I do vote for having sugarcane not following the new ideas for water physics. I like underwater farms/ airlocks!
Everybody here should read: http://www.minecraftforum.net/topic/1583885-blocks-like-ladders-and-water/ - Making fences covered by water is as simple as extending their data value. These data value would then be used by the client to render the water and by the server for its water flowing code (to see the block as water (or air if no extended data values are there) instead of fence in that codepath so water will flow through it). The most complicate thing would be to tell the water flow code that it doesn't have to give water data values to the fence but extend the fence data value, but that shouldn't be a big deal and when done it should be easily extendable for other blocks.
This is not a bug. The only reason painting's and item frames are not affected by water is because they are not blocks