(The [[Known Issues|KnownIssues]] list has some separate items currently. So check that out too.)
JSONs
The defaults need reviewing.
The seeds for the the different dye plants can't be obtained without cheating.
All five tiers of the Infernum plant give the same amount of essence.
Mods should have separate address spaces, to prevent name collisions.
Features
Add fluid capabilities. At least to the tank, but then all of the irrigation stuff.
Fire events for planting, growing, fertilizing, etc. Probably subclass the Forge events.
Add support for detecting liquids, fire, skulls, and other atypical blocks. For examples, sugarcane can be planted without water nearby.
Set the documentation or website up so that we can accept PRs or contributions.
Expand compatibility. For example, MFR machines.
Enable weeds to actually be a threat.
The Journal and JEI interfaces need updating.
Misc Fixes
The water_pad is not working 100% yet, so there's no workaround for supporting plants that grow on water.
Grate rendering and bounding boxes aren't correct.
Need to check for other client side lighting information bugs.
Stacking issue with seeds from the analyzer versus crop sticks.
When picking plants from a list (spawning, spreading) the code often favors items from the front of the list. That needs instead to be a fair weighted random pick. Maybe add a helper method or class. (Cache the work.)
Redstone ore that is glowing is different from normal kind, and so is invalid for the redstone resource plant.
The Sprinkler irrigation doesn't respect bonemeal: false. Oops.
Crop sticks won't replace grass and other such items when being placed. Instead they get put next to them.
The Sprinkler could cache what it has found and search less often.
The irrigation multiblocks need review.
Water particle effect for the sprinkler's target.
Porting
Look into how big the changes for 1.11 and 1.12 are.
Wishful ideas
Fertilizers with different features.
Using consumable fertilizers in the irrigation.
Plants affecting the player when the walk through the crop.
Variety to the crop sticks. For example, supporting larger versions of normal plants.
Instead of harvesting resetting growth progress to zero, have a difference between initial growth and regrowth.