You will probably not find a piece of software that will do everything you want. Instead, you'll likely have to rely on several different programs.
This is good news and bad news.
I understand you're a messy person. Adding more programs to keep track of might seem like a bad idea, but I've found it's usually a question of spanner vs hammer. You need more than one tool to get the job done... Sure, you could probably drive in nails with a spanner but it would waste your time and degrade the final result...
I've also added sections about handling mess at the end of the answer (I'm messy too!)
Most writing software that isn't opinionated about your characters (MS Word, Google Docs, Scrivener) will of course allow any number of main characters. While software designed to help with characters and story like Dramatica Pro will not.
I recommend combining and utilizing parts of the software offers like the one from Dramatica.
Maybe you can create one project per main character and then combine them, trying to find scenes that can do double duty in more than one project?
Yes, doing this will not make it possible for you to use the program 100%, but I've noticed that you pretty much need to clone the brain of people like the Dramatica people to be able to use their theories 100%...
Instead, view it as a smorgasbord and pick and choose what you need/want/what works.
This is one of the areas you mention where I use several different programs to do different types of timelines.
I use Excel to create an overarching timeline for "the big events" in the series of novels (e.g. events on the "worldbuilding-level"). I use Aeon Timeline for doing a bit of the same in one file and then I set up the timeline for each novel in separate files.
I use a program called yEd to brainstorm and untangle cause-effect relations and parallel events and so on (check out layouts in yEd!)
Then, in Scrivener, I've added empty documents (not included in the compilation) that state the day and time. E.g. a document with the title "--- Day 1: morning ---" followed by the chapter folder(s) for the chapters taking place on the morning of day one.
I'm not sure there is a program that will give story advice like you describe and looking at offers like Grammarly that does the same for grammar and spelling I'm not sure you'd want one.
In my view, either we have crap AI that can do this for us badly, or we have top-notch AI that won't need our help writing novels... So I'm saying, so far, thankfully, no such offer has presented itself.
That doesn't mean the help doesn't exist out there, it's just rather in book, blog, and forum format than as a piece of software.
I've moved from Scrivener (that did a great job on desktop, failed miserably on iOS) to DokuWiki (and won't move back even though I now have a MacBook so I have the desktop experience while out and about as well).
I especially find the templating and the linking of a wiki essential to keep information connected and available and to help me organize the information I want to provide for different kinds of worldbuilding.
I also use the wiki for character information.
For worldbuilding (and character building) I've also come across Campfire (there's two versions, Pro for desktop and Blaze as a cloud service), but I haven't tried it out and never used it in a project, but it seems to contain a lot of useful functions and info prompts. Here's a nice demo. (Hm, and watching this demo again I'm realizing Campfire Blaze has a lot of what you're asking for... except for the Story AI though...)
Being a messy person
I am a messy person.
What I've done is I have two places where I keep information: my Dropbox and the Wiki.
Sometimes I'm forced to add info elsewhere, but then I try to force myself to move it into a file in Dropbox or the wiki ASAP. (And my success in doing this is varying... but my goal is to keep all information in Dropbox or the Wiki...)
I suggest creating a folder structure in your file system that makes it easy to know where different kinds of information belong.
You need to adhere to the true and proven adage of chaos fighters everywhere:
Each thing in its own place!
This means, if you have lots of things, you need lots of places. Fortunately, when dealing with files on a computer, you can create as many folders as you need. Create a logical system that lets you remember where everything goes and then stick to it.
Use a service like Dropbox or Google Drive to be able to access these files from your computer, phone, and/or tablet. Make sure you back the files up! Cloud ≠ Backup! (Regularly verify the files can be restored from backup!)
As an example, I create the below folder structure for each of my projects:
- Analysis — For plotting and so on
- Research/Articles — Project-specific articles and research
- Project planning
- Pictures — Many different subfolders for history, clothes, vehicles, etc. Some of the most used are:
- Editing — first, second, third, etc, drafts of the story + editor/beta reader feedback
- Any other folder that doesn't fit in the above categories
I've also created a folder structure for general creative writing information. Sometimes the two get blurred, for instance with the "Research"-folder. I have a general research folder as well and it's not always obvious what goes where, but if I later find I have general research in a finished project, I can always move it out.
The most common format in the research folder is the PDF file. I save/print articles from the web to PDF so they will survive site changes or even sites getting closed down. Other folders would have formats specific to the programs I use, or text files, or even Office 365 files.
Having search functionality also helps (Spotlight, Windows Search, Google for Docs).
Mac OS also provides the possibility to tag files and view the tags in finder folders. This helps when I need files from different parts of the folder system. I have a creative writing tag containing files from both general creative writing as well as files specific to my current WIP. I'm not sure you have similar opportunities in Windows or on Google Docs.
But really, I AM a REALLY messy person
Me too. I have ADHD.
Sometimes there's just one solution. You need to accept that you are messy and that there will be creative chaos, and that your novel won't be as perfect as it was in your mind, or that your process won't be a dream project.
We all improve as we go. Experience will improve your process and having had a system for your files for one month is entirely different from having had a system for a decade.
And still, most of us need to accept that it's better to do something that isn't perfect than to do nothing because it can't be done perfectly.