Here are some hard facts I know.

-Given same size, wheels with low inertia accelerates faster. However, bear in mind that small wheels have to spin more to move the same distance, but their radius is smaller too. So we can assume that acceleration property of wheels are somewhat proportional to its weight.

-Small wheels are generally lighter than large ones.
I have two 406-sized wheels which weighs 992g and 1147g respectively. Dahon's 406 rolf wheelset (w/o pantour hub) also weighs 992g. You just CANNOT find any clincher wheelset this light without spending some ridiculous sum of money.

-Small wheels have smaller contact area than large wheels, and their rolling resistance is actually lower than large ones. From the test data I've seen, 406 sized 28c stelvio tires are better than 23c GP4000 tires (They are very good tires and my dad's using them on his road bike)

Conclusion here is that 'good' smallwheelers can accelerate faster than road bike. From my experience, main disadvantage of smallwheeler is its harsh ride and unstable handling which add up to rider's fatigue.

Quantative analysis will be possible with powermeter, but I have not seen anyone using SRM or PowerTap with smallwheeler yet. I know someone with iBike though.