So did you have a specific question ?
The arduino hardware is relatively undocumented. This is because (probably) it's not intended to be used as an education in hardware design, and it's mostly pretty trivial. To really analyze it, you should note:
- Don't assume that part numbering is consistent from design to design (Uno vs Uno Mega, or even Uno vs Duemilanove
- Looking at the actual EAGLE documents is to be preferred over PDF files.
- if you have a question, say exactly which document and/or board and/or posting you are looking at.
- WRT decoupling capacitors, note that there are quite a few of them. Whether the cap next to the regulator in the schematic is actually next to the regulator on the board is a somewhat academic, if they're the same value.
For example, the dual regulator layout issue is shown using EAGLE here:
The two chips occupy the same place; they can not both be on the board at the same time.