1) The chicken & egg problem of console peripherals does not appear to be the problem that it used to be; wildly popular games like Guitar Hero, Rock Band, SingStar, Wii Fit, Buzz and EyeToy all prove that. The PS3 wand, MS camera and Wii MotionPlus will also start from the same low base (MotionPlus only benefits a few games at the moment). Part of the reason is that the cost of software is approaching that of the hardware. Clever developers can either make the game usable without the add-on i.e. SingStar requires Mic's but will use an Eyetoy if one is present; or just target a niche market of people prepared to buy games that use them; probably more people have a Wii Fit board than had original X-Box or GameCubes.
2) "There are now three consoles with completely disparate motion control schemes". Er, and these consoles also have disparate CPU, graphic sub-systems, SDK's, and optical disk formats. At the moment, all 3 consoles offer different controllers anyway, with the PS3 DualShock 3 providing 3D tilt sensing, the Wii giving that +acceleration and rough position.. and the 360 giving bugger all. The cross-platform games; at least those across the PC/360/PS3 systems work through cross-compilers and good libraries that can hide some of the complex details. Dev's will get a hook into a data stream that feeds XYZ position and acceleration from whatever controller - its just in some cases it will more accurate than others. So may be better in the future when all offer accurate controller information, rather than as at present. The Wii is still the odd one out in that it doesn't have enough CPU or graphics grunt to to run simple ports.
"If you can't make a game easily ported to all three, you'll probably limit yourself to just one. And chances are you'll pick the console with the enormous user base guaranteed to have the right equipment: the Nintendo Wii"
If you are going purely on user base, you might target a PS2. Probably not, because, like the Wii, people doesn't buy rush out and buy many new 3rd party games for the PS2/Wii as with other consoles. Many of the Wii enormous user base appear to be using the Wii as a dedicated Wii Play device.
As for the right equipment, the Wii might have a Wii Fit .. or not, might have Motion Plus.. or not, and probably doesn't have the disk-space, CPU grunt or online play capability you might want for your great new game. Making a cross-platform game (PS3/360/PC) still makes sense.