Regarding Atomic Coordinates + Connectivity.
The use of implicit hydrogens should be avoided. They will create problems further down the line when dealing with non-standard molecules e.g. atoms with multiple possible oxidation states, ionic centres etc. Why not enforce explicit hydrogens now? They don't have to be visualised by a GUI, but should be present in the file.
Why are atomic coordinates for 2D included? (If it is needed for compatability with .mol files, then the rest of this comment is obsolete). Atomic coordinates in "2D" are meaningless aren't they (essentially this is a proxy for connectivity, which is already included - so what further information do 2D coordinates provide). Atomic coordinates should either be in 3D or not included for a given structure.