I will be putting this in pdf in my tutorial section and add to as needed.
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It is interesting that when we get into certain habits and techniques, we become quite aware of how often we utilize them when they no longer work.
1) Clicking on an object on the desktop does not bring up the Transform Tool.
See resulting problems under #2 and #4 below for resulting problems.
2) Using the arrow keys to nudge does not always work.
I nudge layers all the time with the arrow keys. However, in PSE6, if I click to add a layer style and thereafter attempt to nudge, it instead scrolls through the effects palette rather than nudging. Clicking on the object on the desktop does not revert it back and neither does minimizing the effects palette (Clicking on an object on the desktop does not bring up the Transform Tool). The only work around I have found is to hit Control T to activate the transform tool before nudging.
3) Zooming with the wheel on the mouse does not work.
I have never zoomed in and out with my mouse, but many people obviously do because I have received complaints by quite a few people. I utilize Control + and Control – (I use the numeric keypad for the + and -) to zoom in and out.
You can change the scroll wheel settings under the Preferences which are found under the Edit drop down menu.

It appears to me that Adobe wants us to use their built in tool on the tool bar to zoom. Clicking on the Zoom Tool allows you to zoom in and out utilizing only the mouse. Once the tool is activated, click on the desktop to zoom in. To zoom out, select the minus button (or hold down the alt key) and click once again on the desktop. The tool also has other options available, such as “Fit Screen” and “Print Size.”
The cool feature I discovered with this tool is that you can drag the mouse (similar to making a square selection with the Selection Tool) and it will immediately zoom into the area selected.
Another option to zoom with only the mouse is to open the Navigator Palette which is found under the Windows drop down menu.

4) Resizing works quirky; holding down the Shift key works in reverse.
PSE6’s default setting for resizing keeps the object proportionate without having to hold down the Shift key. I am in the habit of always holding down the Shift key before resizing and this is no longer necessary. In fact, when I hold down the Shift key, it actually works in reverse and allows me to resize disproportionately. Due to my habit to always start resizing with the Shift key, this is driving me crazy!
Sometimes I am having the reverse problem whereas I would like to resize disproportionately, but the object is locked into resizing proportionately.
In addition, clicking on an object no longer automatically activates the Transform Tool. Control T must be clicked to activate the tool. This can be frustrating for those who prefer to use the mouse only and stay away from the keyboard, although it can still be found under the Enhance drop down menu.
There is an option under the Transform Tool to Constrain Proportions that can be clicked on and off.
5) A grey area appears around an object brought into a layout.
If you drag an element or paper from the bin up into a layout, it will have a plus sign icon in the lower right hand corner of the layer palette's icon (yea, confusing) and if you hover over the plus sign it indicates it is a "frame" layer. In addition, in the blending modes, it indicates it is "pass through."

I have determined that this is to be utilized with the built in projects in PSE. Under the Windows drop down menu, choose "Content" to open up the palette. Choose "frame" or "theme" to integrate the layer with the plus sign on it into their build in frames and layers. Now try adding some of the other options from that palette. Ick. Someone needs to show Adobe what real scrapping is supposed to look like. Are they trying to do what the "simple" programs do? Why? Shaking my head here as it makes no sense.
Bottom line: Continue to drag your papers and elements either:
1) From the desktop down to the layout in the bin; or
2) Directly from one file to another (as in my first layout tutorial) by utilizing the "tile" setting under the Window drop down file.
3) Import elements using the “Place” feature under the Edit drop down menu.
Although this is less convenient than importing directly from the browser (XP or ACDSee), it does import the title of the element as the name of the layer which is very helpful when giving credits.
Do not: Drag from the bin up into the layout, unless you really like your papers to be reduced to small areas of useless pixels.
6) PSE 6 does not allow for extended desktop space.

7) Currently, additional styles and actions cannot be sorted into groups. I believe techy people are working to resolve this.
8) The dark grey interface is not pleasing to everyone’s eye and will take a long time to get used to. I found no way of changing it.

However, as always, you can change the color of the desktop background to any color by right clicking on it.
9) The icon to tile windows is gone. I used this all the time!

Now it takes me more movement to tile by go under the Windows drop down menu. Because of this and several other things outlined above, it makes me feel like Adobe is trying to make me use the bin.
10) No custom angles of drop shadows.
I understand they took this feature away several version ago. There are quite often times I do want to change the angle of just one drop shadow different from the others.
The only work around I can think of is to put the element in a separate file. Apply the drop shadow, simplify the layer, and bring it into your layout.