I think you're taking the moddability for granted when it has really happened to be just a nice bonus.
If you need override scripts to handle custom spell effects or new mechanics, then you need to look elsewhere, because BG is not the right place for such things. The fact game's AI is also a script is bad enough already. You just don't use scripts to implement mechanics, you either code them into engine or you pick a better engine.
It may be seen as advantage by some - that everything can be scripted, - but BG is not a good example of how you make a moddable game.
Whether BG has the most appropriate form to be modded is really neither here nor there. Of course it wasn't meant to be altered. I believe games are not meant to be poked around in any more than books or movies. They are authors' works, and the more successful they are - artistically, not commercially, Imp - the more coherent and inseparable their elements and logics endure over time. They do not require any additions. But that's on the authors' side. To us these games are something else. We didn't make these games, we grew up playing them, and we present our own creative work in their genre. Someone, whoever it was originally, developed the basic tools, others took them and improved them, and now modding is our earned right. Why stay with and within these games? Why not take a different engine? Because a different engine means a different game, and we have fallen in love with this one. And as far as making computer adventures goes, I know there is, unfortunately, no alternative. More powerful tools, sure. But there is no isometric game out there that has such beautiful visuals, music, so many interesting concepts of places and characters, one that is also relatively unassuming in its outlook, features no very specific setting and readily accepts new adventures. All other RPGs are either first-person, which has its advantages but mostly at the expense of detail (e.g. Elder Scrolls, Vampire: The Masquerade - Bloodlines), or have highly particular settings (Shadowrun or the new Torment: Tides of Numenara), or use 3D models instead of unique backgrounds (Neverwinter Nights), or they are just small-time independent projects with stupid anime or pixellated pretense for graphics.
To my mind, we are all huddled inside this creaking and much too lived-in arc of old-school creativity on a flood of mass-produced fakes. More plainly, I think we are here because there is just nothing that compares in visual and audial beauty, harmony and originality (of concepts). Gameplay balance, custom classes, clever scripts - this we could insert ourselves, given a powerful engine. But we don't want to either play or create for games that are dull and ordinary and ugly. Most of us are probably in our 30s and 40s, and we have lived to see beautiful and inspired games of all genres, not just role-playing, in the 1990s and 2000s. But now we are caught in a modern production values trap: small companies cannot afford and large companies do not dare to invest and risk serious money over looks and sounds and concepts that would be both original and skilled, realistic. Weird cartoons - sure. Just watch the Disney Channel and try not to throw up. Presumptuous AAA slickness so expensive to make, it has to be handled in kid gloves? Also available. But there is a distinct lack of affordable and skilled creativity on the market now. It is true that people like Mark Morgan were exceptional even back in the day, but plenty of games had less outstanding yet still interesting composers. Now the old guard is really getting old and not inspired by what goes on - and who can blame them? And the next generation of artists and designers has no real skill and a timid imagination. They have been brought up in reverence for accomplishments they do not even dream of matching. As Imp says - make something new and you might ruin something from 10+ years back.
All I can say about that is, to hell with it. If we, in this stretch of our lives, each for our own reasons, involve ourselves in fantasy adventures for this engine, then let's quit being so abashed about it. We do have one resource to fall back on that was no available in the glory years - a fan base of people who accept and expect the game to be modified. We have to live with the fact of not owning our house, so to speak, and this results in a painful cognitive dissonance. But by the same token we know that we owe Beamdog no special reverence. It's nice that they add new functions, but they are not doing it for us or with us. So while we can't shake up and clean up something like the scripts hierarchy - Beamdog owns the product, after all, and it may not be worth it - we should not hesitate to make and advertise sweeping changes. Let players learn to take the responsibility for what happens to their installations and playing experience.