The Eagle autorouter is a tool, a good tool, but with any tool it is up to the user of the tool to use it intelligently.
I disagree with those who say you shouldn't use the Eagle autorouter. You should use it but intelligently. First, route any traces that are critical: high-speed clock lines and the like. Then, use "net classes" to specify that certain nets should have thicker traces. This tool (net classes) is pretty rough and could be better but is better than nothing. Then, let Eagle have at it on the rest of the board.
You can always "do better" than Eagle on small-to-medium boards and come up with prettier or more sensible layouts, but you usually don't gain anything, just a prettier layout. You do, however, lose time. If your time is worth nothing, go ahead and route every board by hand.
And don't ignore the value of part placement. There is nothing the manual router or autorouter can do to overcome poor placement of parts. Put that crystal oscillator right up against the microcontroller. Same with the decoupling caps.
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The Ruggeduino: compatible with Arduino UNO, 24V operation, all I/O's fused and protected