Nobody has figured out how to randomize the starters or edit script related data at this time; it needs to be researched by the community before it can be added to pk3DS.
ExeFS editing requires an exefs.bin to be unpacked and set up properly (ie, ".code.bin", not "code.bin"). The Pickup Editor edits the Items obtainable via a Pokémon's Pickup Ability, arranged in a table.
Few updates to the source:
Added Personal Randomizer options, X/Y bugfixes
Added In-game badge specific mart editing (previously was just the special marts), also added X/Y mart editing.
Also changed the way the program finds exefs data locations instead of using static offsets; have yet to test if it works for any 1.1/1.2/1.3 patch exefs.