Gave you rep for this project.
"Smallest plant" is definitely a niche worth filling, and I love the fact that you're actually trying to do something different.
If you're "serious" about pursuing this, I'd suggest trying to do your selections for two factors (only): Small size and potency. (IE there is nothing worse than low yield AND low potency, and having really high potency "nanoplants" is a pretty worthwhile goal, I think). Once you've dialed in the smallest possible plant genes, you may want/have to introduce new genetics to boost potency.
In terms of germination, two tips: First of all, as you probably know, early harvested seeds tend to have low germination rates. You really want to harvest as late as you can if you want to create viable seeds. Next, light intensity matters here. If the plants aren't getting tons of light, the seeds may have low viability.