Lots of good stuff right there. I think the only thing I didnt really cover at all in my "collection" demo much of what you mentioned about the music and adding / removing characters from a caterpillar. I agree that using a more "natural" way moving instead of wizarding around makes games seem that much more "polished". That "natural" way of moving I tried to incorporate into the "collection" also. Such as opening doors, then having the entire caterpillar walk into the door and fade out automagically as they do. Other things like caves (theres only one in the demo) the characters also walk in. Most of what I do is just moving between maps.
Scripts
The style I have decided on requires scripts to pull off. I have the whole caterpillar also walk completely off the screen, then on the next map, I have them walk from off the screen to on screen. One of the scripts I wrote for XP (caterpillar based on Zeriabs) allows characters to "walk off the map" specifically for the purposes you mentioned. Scripts also allow events flagged as a "\door" to close once the last Caterpillar Actor has walked out of the door. Or at least play a sound if the door is not visible because its at the bottom of a room and not the top.
Eventing
The main thing I like about the caterpillar (the one I did based on Zeriabs) was that it uses actual events as your followers. This allows total control over the movement of each Caterpillar Event. I put in a ton of extra stuff to allow the caterpillar to take a step backward automatically, pile up, fade in and out, (includes easy scripts for fading events), and other stuff I thought should have been included in XP but was later included in Ace, such as having the Player graphic turn toward or away from an Event. Another little script I wrote was to allow an event to move directly to a new location, like Jump, but without jumping. Its useful if you want your characters to move around in a direction that isnt one of the defaults of up down left or right, or the diagonals. Such as a Wizard that launches a fireball that isnt in a straight line, like at three characters at once.
Pauses
Totally dead on and absolutely right. The way that a character speaks is far more important than what they say. Sometimes sounds can be useful to "give a character a voice". I enhanced Wachungas MMW script so it now plays sounds per letter, or every 3 letters, depending on how you set it up. Although I put it in and thought it would be neat, I dont use it very often. That may change if I find better sounds though.
Cutscenes
Time and time again, cutscenes are not about the dialogue, they are about Body Language. 90% of communication is done through body language, and Cutscenes really give game creators a chance to show off their eventing skills and express that body language. It is still very possible to do in RPG Maker, and almost somewhat easier. Cutscenes are more than just having two characters stand face to face and spout dialogue at each other. Movies dont do this, why should games?
The default XP engine really needs some enhancements to be able to do what you describe. Even fading in music, or a crossfader would be great. Fortunately, since we can script for XP and up, there are a lot less limitations, but at the expense of greater skill required to create a game.
So, just out of curiousity, what scripts are you using to pull off all the techniques that you mentioned?