Firstly, I'm not posting here as mts site staff, but as a creator and user. (I'm also not aware there's any plans to change upload policy at mts, in case that's what you're concerned about – the current way to handle overrides (i.e. what you describe: creators must state what resources they're using, so that downloaders have a chance to sort it out) is tried and tested and seems to make sense. Any other concerns regarding mts, please post there in Site or Creator Issues.)
Apart from what velocity says about large-scale vs small-scale mods, there's also the problem with overriding objects that have tuning for completely different aspects – there is no logical reson one wouldn't want to, say, have children be able to use gardening plants and at the same time change their harvesting states. Or have several different custom interactions added to the same object (say, dancing on tables vs. sitting on tables or whatever). But by overriding, this isn't possible – everyone would only be able to change exactly one property of each object (or manually splice the mods together).
Also, overrides always come with the joy of having to check for differences with every single patch Maxis will publish .. if they keep up their current rate, I'm rather not so keen on that. Scripting might offer the big advantage of being able to keep using the same script to modify whichever the current version happens to be, without touching the rest of it.
Also, for all I can tell (I don't remember very much about TS3 tuning), tuning in general is vastly more powerful in TS4. So trying to make it work as hassle-free as possible would be something that has more of an impact now than it would have previously.
