Whoa... don't get me started on that topic!
Oh, we wouldn't dare!

Consider, though, things like the pin spacing goof that has been perpetuated throughout all the Arduino boards
Well, that is the risk in beginning a "standard".
not to mention the mounting holes which, by their placement and lack of a "keep-out" zone for the traces, are 98% useless.
I do agree.
You can however use these:

or these

For example, why are maybe 6 bits out of an 8 bit port connected to one contiguous connector space and the other two somewhere else? Makes it a mess to use as an 8 bit PARALLEL port.
Ask
Atmel - who designed the
clearly essential serial interface to use pins 0 and 1 of an 8-bit port. No fault to Arduino.
And, pin numbers! Why "Pin 13"?
Err, why not?
I want to know what PORT and what BIT the pin is, not have to constantly bring up the PDF of the board to find out which pin is what (you'd think I would have it memorised by now).
Because people (are intended to) use this as an
educational system, focused on the
application rather than the hardware minutiae.
And, why "pinMode" and "digitalRead/Write"? What's wrong with PORTB |= _BV (5);
I think that one
really speaks for itself.

When something is dumbed-down to the lowest common denominator, nobody LEARNS anything.
Admit it. You, like I, came to Arduino with
complete knowledge of microcomputers and even assembler.
So why are we even interested in them if they are so far below our dignity?
Because they
are a really neat modular system that you can use for rapid construction, just like the STAMP(, the PICAXE and its other spin-offs) - but more powerful, generally cheaper (
vastly cheaper in terms of the clones) and not quite so dumbed down.
Maybe AFTER you can explain to me why my boards (both Arduino and homebrew) all work fine WITHOUT caps.... 
As Mike would explain, there is a difference between "working" and "working within specification". Crystals have specified loading capacitance for correct, reliable and
stable operation. If you operate them outside of that specification, relying on the (significant) pin capacitance of the MCU chip, then it probably
will work - but just don't expect it to work to specification.