The theories (with physics supposedly backing this up - don't ask me to explain it) are larger wheels are smoother feel and cover more ground for a given pedal revolution - ie, your gear will actually be higher by a hair with 700s than with 559s, all other things being equal.

The pluses for the smaller wheels are improved strength and faster acceleration.

Imo and experience, the big plus is they put me lower to the ground and increase my standover height - both pluses in hop on & off mtbing and urban riding with traffic lights, unpredictable humans, etc.

I will say I noticed the biggest increase in commuting speed when I went from SS toi a derailleur bike. I never clocked road vs mtb but I am thinking the mtb would be a tad slower. Hardly anything I'd be concerned with tho, especially on the commute. Besides, the MTB saves time in hopping curbs and whatnot.