I think TheValeman was just pointing out that the original intent of the N64 cover project (as it was started long ago over on Cheap Ass Gamer), was to get the covers to preserve the original game box art. i.e. so that the games appear to be in the original boxes.
Custom covers are great and I like your template. Choices are what make the project so much better.
Some of us prefer to preserve the original artwork/manuals/labels. This does not take anything away from your work or criticize you, everyone has their own personal preference.
Its creativity like yours that allows there to be covers for games in which original artwork no longer exists.
On the other hand, a LOT of people here are looking for custom covers to replace the originals because they don't particularly like the cover that came with their games, or they simply want their PSX/Dreamcast/Sega CD/etc. games to match the newer PS2/XBox/GCN cases.
Good job on the custom template.