There are several model editing techniques (for AC:CF):

"ITEM_Tool" can be used for recoloring existing items.
"LMT" can be used for editing existing items, changing sizes, orientations etc. You can't tweek individual polygons.
These are my tools, but were abandoned because of lack of interest.

"SZS Modifier" does similar things as LMT, but has other features for individual polygon editing.
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Using MilkShape3D was an attempt to get more people interested in model editing. It can be used for creating brand new 3D models.
I used it for the round spheres for the spinning PokeBalls, which I then merged into an existing .BRRES

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Bottom line: I've given up trying to make general purpose tools for 3D editing. There aren't enough people interested in it, and not enough is known about the BRRES details to make a totally general 3D modelling tool.

If you have an idea for a new cool DLC, please try the existing tools, and/or send me an email.
The 1 year anniversary is coming up, and hopefully we can do something cooler than the DLCs released so far.