I see, but does the plan include a way to store them in a package file? Most games do it like that, because tons of tiny, uncompressed files waste a lot of space.
If I was a commercial company and wanted to sell NeoLemmix, then I would certainly do package them and either keep them in that binary blob or would extract them upon installing the game. That is perfectly fine and totally the way to go forward, if one has a game that won't be modified any more and all players have to be satisfied with the current content.
However NeoLemmix thrives mainly due to its custom content. Many users want to design further level and play them, create new styles and even customize the appearance of the main menu. If we would package everything together, then noone could publish their new content themselves, but had to ask me to addit to the bit pack. Then everyone would have to download everything again, even the content they already have. That's certainly not perfect either.
On the other hand, having lots of small files allows fast and easy updating with new content. Yes, the initial installation takes long, but on the long term, it will save us all lots of headache.
Up to now, NeoLemmix did sort of a middle way: Have several packages with either styles or levels. However over time this created problems: Several different versions of styles floating around, noone knowing whether their version is still up-to-date. Level using an old version while the player has the recent one (or vice versa), which yields to errors that noone knew how to fix: Is it a bug in the player, or a bug in my own style file or a bug in the level? Some level packs relied on internally saved style files and got buggy when the user had a different version of the style in their style folder. Some other packs becoming buggy because they relied on an external style, but this style got updated. And the player of these packs wouldn't even be aware of all of this, because they had no way to tell what the level pack requires resp. what was built in.
None of these problems would have been nearly as bad, if everything was easily visible to all users.
And two final remarks:
1) Most of the bigger fan-made projects that allow customization go along this way and have lots of style files, ... Admittedly they usually hide it better, e.g. by displaying a nice preview video while extracting all the files, but all those small files are there.
2) The NeoLemmix files aren't really that big. Currently all styles combined take about a few dozen MB. With usual hard discs having hundreds of GB, that space is negleglible.