The ones I left out are either old ones that I never got, new ones that I haven't saved up enough for yet, ones that I probably did have in the timeline but took out to get it down from 27 pages to post it here, or ones that I haven't had time to think through yet. It's a major work in progress. Ideally, I want to fit every game in, but obviously for some, it's just not feasible. However, I did get Mario Teaches Typing in, so hopefully there won't be many games missing in the end. Hopefully I'll be able to play the older games on the Virtual Console and the newer ones... well, I'm hoping to be a film director soon, so that should pay enough. I'll try to put the full timeline online somewhere once I get it into a more finished form if anyone wants to check out the whole thing and add their comments. Probably the most noticeable games I've never played are Partners in Time and Super Mario Land 2 through Wario Land 3.
I haven't really come up with a theory for Bowser Jr. yet. There's obviously something different about him since he looks so much more like Bowser than the other Koopalings, so that difference is probably what kept him from being hatched until the right time. Maybe he's the Chosen One or something. Star Wars does have a noticeable influence on my full timeline now that I think about it.
As for the Thousand-Year Door thing, I couldn't really remember the ending of PM:TTYD, but I was planning to make something up about what happened a thousand years after PM, where there would be some new thing behind the door, and then as I was filling in the birthdates of hundreds of future Booster generations, I decided to throw something in a million years in the future just to stretch the timeline out. It was mostly a joke, really.
Some of the powerups are obviously magical, (Raccoon Leaf, P-Wing, Magic Whistle, etc.) while some are more natural. (Cape, Anchor, Music Box to some extent, Hammer Suit, etc.) There are also probably many variations on all of them. We know just from the RPGs that there are Mushrooms, Super Mushrooms, Ultra Mushrooms, Max Mushrooms, Life Shrooms, 1-Up Supers, the Mushroom that turns you into a mushroom, and many more, and the existence of the Invincishroom shows that new varieties can be bred. In fact, the trick mushroom you got from the Goomba nephews was probably a variety professionally bred and sold to joke stores. Also, in SMRPG, there were Mushrooms that completely restored all HP and FP. Following the Nintendo-console-adjective tradition, (SUPER Nintendo, ULTRA 64,)I guess those could be Virtual Mushrooms, Mushroom Advances, Mushroom Cubes, or DMs. But there's probably a better name. Anyway, I think the magical ones were created by Magikoopas at some point, but a problem arises - If they're making them now, it must be a pretty well-kept secret. If they were made a long time ago, then why are there still so many? This is fun!