OK, so I'm probably an idiot, but it just occurred to me that setting objects up with an alias is pretty much the same thing as setting them up with the standard object reference properties and so forth. For example, I could place some objects, set them up on an xMarker with an enable parent, and either make an alias and control the xMarker with that, or the standard Object reference property and control it that way. Both will do the same thing, so why would I use an alias as opposed to the regular Object Reference property, especially if I'm only enabling or disabling it, and it basically won't change? I think I've made a crap load of aliases that I simply don't need, and should have probably been using Object ref properties. For an NPC that you might want more specialized control over, yeah, I can see it, but for standard objects I think I've been wasting my time.

So, should I go through the nightmare of converting all these aliases I have made to Object ref's? or will I be Ok with the aliases?

Aliases are more for use in quests, but they are still useful in scripting. For one, it allows you to attach scripts, add factions, add keywords, etc., to objects without actually editing them. They are also useful for dynamically grabbing ObjectReferences for your script to use, as well.

If you don't need to do any of that, or you don't need for your quest to have a pointer to that object, than a basic ObjectReference property is fine.