Oh your right, I read your post backwards.
Your right, luckily my lens doesn't have that shallow of a depth of field. You CAN use composite photography via photostacking to increase your illusion of depth of field since yours is so shallow...
if you wanted to you can use the mask layer function exactly the same way to create a composite image where the subject is entirely in focus.
I dont know really much on this photostack application or program or whatever it may be so I honestly dont know whats "easier". for me the mask layers in photoshop gives me all the control I could ever really need..
I guess the # of photo's it'd take you to get a focused subject matter would depend on how long your subject matter is in relation to your plane of depth of field...
what you really need to fix this is a tilt shift lens

that allows you intead of having a DOF plane that is perpendicular to the ground you can actually tilt the lens so that your plane of DOF actually is parallel with the subject, so instead of a foreground background difference you'd have a verticle difference allowing you to completely focus on say... a pygmy drosera.. that didn't have alot of verticle height...
but if you say break down your subject matter into say... 3 different focus levels, with photoshop you can easily merge those 3 to complete a totally focused subject...
you'd use your mask layer on each layer and you'd take away the unfocused area's of the subject matter...
so with 3 stacked layers you'd end up with only the focused area's being visible.
this amount of control allows you to also change light levels and do color correction on whatever specific parts of the plant you'd need to do, so if one part had highlights there blown out you wouldnt have to adjust the entire photographs histogram...
-Chris