(Sorry everyone for me taking so long to reply for your post, it was rather hard to think of an answer.)
I choose to politely disagree with your post. Having a clear vision about what to do is good, but I don't agree with stopping the development of the game for that reason. I might see some inspiration on Youtube, ICU Gigasoft, etc. during the development and I will surely add to to my to-do list(this reminds me that I promised I'll add the main features of the game to first post, but I don't think that I'll do it now, maybe later. For now, I'll just mention that Yoshi will be one of party members.)
It's very tempting to jump right in, but if you don't have a clear vision and don't do everything you outlined, the project will take longer than expected and you will end up spending a lot of time revising what you have down already, which will greatly hurt your motivation.
Partially true, but you didn't mentioned that making a mostly complete list of things to do will probably take months, and when I'll actually start developing game, I will most likely modify most of these things and scratch some of them due to me not knowing RGSS3, plus I don't really mind changing what I have already. If I'll nonstop implement new things, I'll tired of porting tilesets and sprites and making events for them. Also, the player will be more impressed if the all areas they visit are in the best quality that I can make.
However, I'm speaking from my own experience as I have made the same mistake several times and don't want to see others fall into the same trap.
My game is RPG, not MMORPG. It uses RPG Maker, not Eclipse. My game has story(it's a RPG after all), your doesn't(or at least not in-game). My areas will be short and filled with events like in original Mario RPGs, not long and bland. And most importantly, you actually have to code things, I just copy-paste scripts.
Therefore you can't compare my game to your game.
For the screenshot you provided, don't try and merge the elevated-height cliff and the lower-elevation ground with a path like that. It looks kinda cutoffy and weird. If you want to maintain the transition of going from a higher elevation to a lower elevation in that map you should utilize the vertical stairs instead to make it more clean.
Mapping is a lot of working around the problems with the tileset to make sure you have absolutely 0 graphical anomalies and cutoff.
I posted that screenshot just to show the tilesets and that map was going to be removed,
but I can still thank you for pointing that out, to keep it in mind when I'll actually start making maps.
Regarding game progress, I started making some more areas(just Mario's house outside and path to first place you'll visit in this game), but I needed to change the game resolution to something smaller, to prevent myself from making extremely large areas and to make this fangame feel like a real Mario game. There's one problem with that, though. I tried to make the resolution smaller by putting a line of code before Main call or whatever it's called, I changed the game resolution to 384 x 354 but there is small line of transparency at the very bottom of screen. Also, fonts are too large to fit and they don't look that good when resized. And even if I'll manage to fix these problems, the resolution is still 384x354, compared to DS's resolution of 256x192. Setting the game to this resolution causes the up side of area show on bottom area of screen. So I guess I'll just deal with resolution of 384x354.
EDIT: I changed the font to "MarioLuigi2", but now the following symbols: , ' " look all too small, nearly invisible, so when a sentence reads "Hello Mario, it's a nice weather, isn't it?", it looks like "Hello Mario its a nice weather isnt it?". I tried editing the font with some font editors, but they are all too complex. Any suggestion to solve this problem without changing font height (and thus also game resolution, which I don't want to change) will be appreciated.
EDIT2: Regarding my resolution issue, while I belive that except small font symbols it's solved for the in-game part, it would be nice if I could somehow display the RPG Maker's level editor at 2x size or something, so that I wouldn't design a long level and then, in-game, with smaller resolution, find out that it's too large.