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Rank the elements by importance to you so I can prioritize my work on features. Drag the elements into the grey boxes. If you are done, save. You don't have to sort all elements. Just pick those you are sure about. Feel free to ask questions at the talk page.

Input file and or storage formats

MDL MOL file (Chemical table file for a single molecule)
MDL RXN file (Chemical table file for chemical reactions)
MDL SD file (Chemical table file containing structural information and associated data items for one or more compounds)
MDL RD file (Chemical table file, reaction-data file containing a set of molecules or reactions, and their associated data)
Chemical Markup Language (CML is capable of supporting a wide range of chemical concepts including: molecules, reactions, spectra and analytical data, computational chemistry, chemical crystallography and materials)
Simplified molecular-input line-entry system (a specification in form of a line notation for describing the structure of chemical molecules using short ASCII strings)
Query language for SMILES

Rendering options

bond length
average bond length in pixels
horizontal and vertical margins
relative thickness factor
line width
bond line width factor
toggle hydrogens
toggle implicit hydrogens
force [de]aromatization
different stereogroup display modes
center double bonds
center double bonds which have an adjacent stereo bond
reaction catalysts placement
reaction catalysts placement w.r.t. the arrow
text comment to be put above the molecule or reaction
comment offset
vertical space (in pixels) between the comment and the structure
comment name
molecule/reaction name as a comment
comment size
comment font size factor relative to bond thickness
comment position
text comment position
comment align
text comment alignment
enable/disable coloring
highlighting thick
highlighting with thick lines and bold characters
highlighting color
highlighting with color
background color
background color
foreground color
default foreground color
AAM indices color
color of AAM indices
data SGroups color
color of data SGroups
comment color
color of the comment
atom numbers
show atom numbers
bond numbers
show bond numbers
alignment on substructure
provide a substructure to align all molecules on it
highlight substructure
provide a substructure to highlight in a molecule

Integration and additional features

Save INCHI and SMILES as Metadata to enable searching etc.
substructure search
substructure search (w/wo GUI query editor)
scaffold detection
find a scaffold from multiple molecules, list R-groups
find out whether a molecule already exists at Commons your media repository (just drawn differently)
combinatorial chemistry
define reaction patterns, input molecules and defer the remaining work to the software
integration with Wikidata
use Wikidata for media info for storing automatically calculated values
web-based editor
web-based editor for creating molecules and reactions
server-backend support for Web-based editor
server-backend support is required for heavy operations like cleaning in 2D and aromatization.
web-based editor integration
visualEditor or Wiki-Editor plugin or something that allows people to create and alter formula files during article work without having to leave the page they are working on.
SVG editing
SVG editing to allow highlighting single atoms, or do more creative and illustrative stuff like deriving creating diagrams from formulas.
auto-categorization using remote data
query-support for big databases (PubChem, ChemSpider) to pull-in categories
remote data
query-support for big databases to pull-in everything they know (including CAS, melting points, …)
allow downloading reactions molecules, … in other formats
view in 3D
3D JavaScript viewer

Minimum viable product

Drag here what is required so you would say: “Fine, please provide us with MolHandler!” Note that too high requirements may make this project going to sleep due to burning out the project members. The project's lead categorization would look like this. It is based on what is feasible in the next 2 months.

Let's have this soon

Consider for the long term

Not useful for anything I can think of