Don't know about the suspended ones but in my experience with a standard one:
Short (MTB) towing fork much stiffer than long (700C) towing fork, so much less tortional shudder if you hit a bump on a fast bend.
Yak more streamlined, so noticeably better into headwinds.
Panniers lighter (5kg?) so better up hills.
With Yak:
Have to detach before lifting over a fence for sneaky camping, rahter than just throwing panniers over.
If ride though shallow ditch, get shot out by trailer weight.
Can park bike without leaning it on anything by turning at right angles to trailer.
Parked Bike/Yak makes great back rest for lunch :-)
Steve