I don't really think there's any way to speed up most of it. Nothing is really target-able, so we can't IWT our way around the plots. The best I can do is like Lyonheart does, save the "bad" plants for last, gather up everyone's critters all at once and makes them kill those all at the same time, make everyone do their weeds at the same time, etc. Mostly, I just suck it up and do them one at a time, though.

The only "time saver" I've got is this macro, which is more of a random dailies stuff kind of thing

Code:
/click ExtraActionButton1
/tar [mod:shift] Farmer Yoon; [mod:alt] Andi; Untilled
/tar Black-nose
/console UnitNameFriendlyGuardianName 1
ExtraActionButton1 is more for using the Hammers in Stormstout, but it also works for the poison for the weeds daily and stuff like that. I rarely even get the Marmots daily, but that makes it easy. And I have the mass tilling machine, so I don't really need "Untilled" in the targeting but I might actually go back to using it instead, or swap it with the Seed vendor's name. Or both, who knows.

But, I always use the target for Yoon and Andi to get in and out of the phase. The last line turns on the names over all the plots so I can see what's there with my slaves. I missed more than a few "imperfect" plants because my graphics on the slaves are so far down I couldn't see the wiggling or runty plants or the little weed hiding in there. I have "/console UnitNameFriendlyGuardianName 0" tacked on to my follow macro to turn it off again.