As we all know many of the cutscenes in vanilla were removed from BG:EE because they simply did not meet the desired level of quality. In most cases I'm fine with that; the video for Gnoll Stronghold, for instance, was never very interesting.
The Cloakwood cutscene however, always felt like an important part of the road to the Cloakwood Mines. It's easy to forget what a dangerous and massive forest Cloakwood actually is, but with the vanilla cutscene travelling through Cloakwood had a feeling of having gone too far astray, which I think is the way it's supposed to be. For new players, at least.
Yes, I know that the cutscene only shows up close to the end of the hazardous trip through Cloakwood, but that's the whole point. It's always the last impression that sticks, and it's by the end of the woods the player should start feeling homesick.
Without the cutscene Cloakwood just feels like a sequence of areas that lay far apart from each other and contain many annoyingly poisonous creatures.
On a less important note, the cutscene was also a nice way of warning the player that this is it
- now you're going to meet wyverns! Carrying the cow demonstred the wyvern's badassery.