I'm new to the Arduino ecosystem, so please forgive my question. I'm curious why there's a 1/2 pin spacing between D7 and D8, and the ICSP header is offset, on the Uno? It makes it hard to just grab some proto board and make my own shields.
Matt.
Perhaps the Micro or Mini would work better for you, or just use an ATMega328 on the proto board and skip the Uno. Or use the Proto Shield. Or doctor the Proto Shield files to fit your needs and send them to OSHpark. Lots of options, but history is what it is.
I agree that using a different platform might be more suitable to proto board development. It would be nice to be able to use existing shields, too, however. There's also several ready-made proto shields available, so I'll use those.
Actually, I think I came up with the answer to my own question. The spacing keys the shields so that they can't be connected the wrong way around. Sensible, but a minor pain just the same. 
No, during their last revision before a big build, maybe 10 years or so ago, they screwed up a few things, including the spacing of the headers. That is staying because too many shields have adopted the spacing and will continue to use that spacing for as long as the official arduino uses the spacing.
So you can easily use a proto board to make an arduino shield for UNO but there are plenty of $5 proto shields you can buy. It saves you time to just buy a proto shield with ready made 5V GND in convenient places and some have more features than a plain board with holes on.