From my point I can answer your question with a big YES! Make sure to check out the new version which is in beta testing currently (you can find the download links for version 2 beta files when searching the scribblecode forum). The beta has no thorough documentation so far but things are really not that complicated. But to get the most of it you will need to work with it a couple of hours, like with any software. But Aeon comes with templates for different use cases (fiction, screenplay, legal, …) which will give you a head start.
Scrivener syncing works pretty well (tags, synopsis, meta data) up to a point where you could do your outlining in aeon rather than in Scrivener, especially if timing scenes is your most important aspect for the outline.
For your use cases:
Character Timeline
-
You can easily maintain a general timeline for your character and adjust it as you see fit (I call it the backstory timeline). E.g. important events which happen to your character in one part of the series could be added and then become backstory of the next part, and so on.
-
For tracking the timelines of each part, you could set up separate timelines for each part in addition to the backstory timeline. For not having to switch between the backstory timeline and the current part’s timline during work you could import the backstory timeline into the part’s timeline when due and work within one timeline only. With a bit of filtering, copying and exporting you could then also update your reference backstory timeline with those part events that will become backstory for the next part and start the process over from there.
-
You could also maintain one single timeline for all novels and the entire backstory (all of the events within can however be nicely separated by using the appropriate meta data available in aeon), but that would make syncing with Scrivener difficult in the long run (I assume that you have one Scrivener project per novel).
Plotlines
- Besides the normal meta data like tags (aeon terminology for keywords) and all sorts of other meta data fields, aeon uses an advanced feature called Entities and Entity Roles which you can use for assigning events to Plotlines, characters, places, things, you name it. For example a character can be Participant in one scene and Observer in another, etc. Depending on your settings these roles can be assigned multiple times per event if necessary. So you could have a scene (= event) which belongs to your Plotline A as well as to Plotline B. This is great for viewing your scenes in aeon grouped by Plotline, then by character, then by location, … you get it.
However Scrivener has no comparable feature but only labels, keywords and meta data, all one-dimensional (which is not too bad, to be fair). So you need to map the aeon information to the information types available in Scrivener. I like to use custom-structured tags (=keywords in aeon) for this purpose. For plotlines I set up a keyword hierarchy (“Plotlines”) in Scrivener and then I use keywords like “pl: ALine”, “pl: BLine”, etc. (the method is the same as described in R. Curtis Venture’s very good blog post: http://armadawars.blogspot.de/2015/09/use-scriveners-keywords-to-manage-your.html and I use it for everything: characters, locations, items, key concepts, plot points (“pp: IncitingEvent”, “pp: MidPoint” “pp’: PinchPoint1”, …)).
In aeon when I have an event assigned to “Plotline A” and “Plotline B”, I make sure to also assign it the aeon tags “pl: ALine”, “pl: BLine”. Then, in Scrivener, you can filter your scenes for any Plotline. There are other possibilities as well (e.g. mapping aeon’s Color field to Scrivener’s Label, or mapping Entity Roles to meta data fields), but for me keywords is the most versatile one.
So, how do you do Plotlines in Scrivener currently? Whatever method you apply, there is a feature in aeon which you can map the data to.
And finally: Matt, the main developer, is very friendly and responsive. So, give it a try! (I am not getting paid for this – but really, I should! 
)