Thanks for the detailed reply, Firecat!
I totally acknowledge your point; in that none of these problems are weaknesses of RPG Maker, and that the engine has the tools and capabilities for all this stuff. Naturally though, a new user may not be aware of those techniques (though they're quite simple once you know them).
In terms of teleporting the player around the game, that's actually what I had planned to talk about next week, with a high-level state-machine that guides the player through the narrative, and gives the developer the ability to teleport to any point within the game with the prerequisite variables, switches and items activated.
In terms of your points 2 and 3, please accept my apologies; I think my language was unclear. I can see how I may have suggested these things were programming issues; what I meant to express was dealing with the complexity that arises when you go from a small, short, simple experience to starting to work with many locations, events and other things. RPG Maker's actually a pretty robust piece of software; I hadn't intended to suggest it was a problem with the program itself - but more a beginner user might start to struggle to keep track of things, and I plan to talk about some ways to deal with that.
You're right in that this is very much a "me" problem in RPG Maker, because part of these articles is about explaining that I've encountered these problems and how I dealt with them. That being said, I've seen a similar problem come up with others who are working in different engines, so I assumed it to be quite universal. Evidently that was in error, but still, hopefully the follow-up articles will be useful to absolute beginners.
I'll take on-board your feedback, and try to be clearer in the future about where my examples come from, and about being very clear about how these problems arise from the user's own issues rather than the software itself.
Judging from your profile, you're pretty expert on matters RPG Maker, so any feedback you have would be incredibly useful!