OP's thoughts are similar to mine. Arensito page has done some research on punctuation, but it still requires an AltGr that most people are not familiar with.
I'm also a coder, and I feel the same pain regarding the (), which are used quite a bit even in prose.
I just started playing around and making my own custom layout. My results are here: http://sagez.net/amuseum/layout.htm . I updated Maxwell / Capewell's Java Applet for J2DK just so I can recompile the code. I also added a percentage for each hand. It's striking to see that while Arensito and Colemak claim that, for their layouts, right pinky is less stressed and left and right hands are balanced, their claims are simply unfounded. This is even more exaggerated for coders who use punctuation a lot. (Added a few other layouts for comparison's sake.)
The () issue I took care of by putting it on the bottom row, without the need to shift. Their shifted forms then become []. Another thing is the double quotes, which I feel should not be shifted. Thus, both single and double quotes are not shifted, while colon and semicolon are. Periods and dash should be at the top to facilitate typing IP addresses and decimal numbers. I also moved the number row around a lot, mostly for experimentation.
I do use MKLC for testing. Version 4 does allow you to remap the keys so that () don't have to stick with 9 and 0. However, to bring along the Ctrl+keys functionality, you must edit the .klc in NOTEPAD (simplest program since it saves in native Windows format). Change all the values of VK_ values to the current character. (But first, copy a default layout and jot down the OEM_ mappings.) IOW the common cut and paste commands do not change position between layouts. The bottom four left keys will always be used to cut and paste unless you specifically change the .klc the way that I just mentioned. So whether your layout uses Z or ( in the bottom left key, the Ctrl combination with that button should map to Ctrl+Z. It could be interesting to make two separate layouts, one with Ctrl carried over and one without. Then switch it from the menu or toolbar or Left-Alt-Shift or whatever, depending on whether you're gaming or editing files.
Basically, I learned from all the layouts and find the things I like about each. Dvorak, like many of you, was my first alternative keyboard. I've been happily using it for almost a decade. There are some quirks everyone is familiar with. But the best thing about it is that it focuses mainly on two rows so row jumping is minimized and timing is thus increased. All vowels on one side, I still not sure of. Looks neat, but sometimes too hectic. That's happens to all layouts, though.
I maximized the most frequent letters in the best spots, while still maintaining some degree of rolling and finger switching (though not quite as fervently as other layouts). More importantly to me though is balancing between both hands and reducing work on pinkies, especially the right. As I said, Arensito and Colemak, according to the Java Applet, do not achieve this goal. Dvorak with all vowels on one side obviously strays from this goal. In fact, all three really perform the same in these two criteria. So all this talk about Dvorak being more right-hand-heavy is just trash-talk and nothing else.
Cut and paste is done best with a multi-button mouse such as MX Revolution. Remap the thumb buttons, that is the most efficient way to cut and paste. No looking at keyboard, no switching from mouse to keyboard, no finding the mouse, no going through menus, etc.
