The launcher only gives you an option to enable or disable plugins, which is the most basic of feature a mod manager should have. Skyrim suffers this too, having a distinct lack of any proper tools to manage your mod load order. Where the real issue lies however is the fact that the game seems to lack a proper built-in Mod Manager.
Heck, most of the crashes in a modded Skyrim installation is simply to blame to mod dependency being configured wrongly. Installing a mod that clumsily forgot to rely on the right resources is a common issue of crashes. While not being a modder of the game myself, it doesn't take much imagination from a modding veteran to see where the real issue lies. This seems like a clumsy thing to have happen.
