I'm not really a modder, and this would probably need a major change in how the game handles items, but a "tag" system for easy leveled list/perk changes/additions would be nice. As an example, a perk pack I have installed for FO3 increases the damage of the various Chinese weapons in the game. Now, I'm pretty sure it has to have a list of what weapons to give the boost to, which rules out mod-added weapons that would fit. With a "tag" system, it could just automatically apply tags to all weapons with the "chinese" tag. It could also help out in some quests, with one quest from FO3 using a specific list of weapons for a "fire-based solution" to one specific quest. And you wouldn't have to worry as much about breaking leveled lists if you want to add, say, new raider armor, just tag it and it should automatically get introduced to the list
Just so you know, the way MODs work with Gamebryo is that items that exist in the original game database are OVERWRITTEN by copies of the orignial that are edited to change the stat you desire. They are NOT the same items with changes applied but actually NEW objects. This overwritting process is what causes the "load order" to be important (last overwritten object loaded is what the game actually uses).
While lists like you mention are possible within the GECK they are handled just like every other object and are an entry in the DB that the mod adds. You CANNOT alter the orignal game data in any way via the GECK itself....you can only copy it, rename it and overwrite it with a mod file entry.
For example, I wrote a simple mod that adds the Nuka Grenade and the Unique Flame thrower to the Pyromanic Perk weapon list (the Flame Thrower was a bug that was never fixed, and I just think the Nuka should be since it DOES generate a fireball effect). It requires a mod file that adds the 2 new items to the list and then overwrites the original list when the mod loads (after the main game file).