UrbanVoyeur. I don't think I have had boot times that are twice as long. I will time them, when I have some free time. For me the biggest performance factor has been disk read/write times. I didn't see any major differences between the two, may of gotten a bit faster with the Arch kernel. To your comparison of the TP2 to the PogoPlug Pro (black).. The PogoPlug pro should be more responsive and faster (depending on situation) since it has 2 cores versus TP2's single core.
When booting, have you had much luck controlling the leds ? Mine blinks red, and haven't had any luck in changing via /sys/.../leds.