I've just started trying out a couple mods, and was curious as to why nothing in-game acknowledge mods that are active. 

The problems arise when a mod feature isn't functioning as it should, and you are left scratching your head trying to determine why:  Was the mod placed in the proper sub folder, or sub-sub folder?  It the mod incompatible or simply poorly conceived?  Are certain criteria not being met?  Do the stars need to be in a specific alignment...?

I would prefer to have some method of installing mods from the game itself, as opposed to relying on third-party launchers (no disrespect to the authors of those apps, but they tend to have a hit-and-miss functionality that changes with each game patch).  Also, being able to verify a mod is, in fact, loaded would be a simple way to eliminate a lot of guesswork.