> It’s so confusing, why shouldn’t I just be able to follow his story from beginning to present?
> (I’m using Batman as an example but really I’d like help understanding how to follow comics in general as they’re all laid out this way, with overlapping arcs and timelines and such)
This isn't entirely how comics work. In general, it's not the only way other mediums work either. The REQUIREMENT that everything follows a strict, traditional/conventional 3-act structure (beginning, middle, end) is self-imposed and not necessary for good story-telling. The "beginning" of comics happened decades ago and the "end" is nowhere in sight; comics are perpetually stuck in the "middle".
You're already used to non-traditional narrative structure; it's used very often in other mediums. Why does Star Wars get a pass but not superhero comics? Did you see how Darth Vader "became" Darth Vader before he was introduced for the first time? Do you refuse to watch/read/play anything that will potentially have a prequel and ruin your "sense" of chronology? Did Memento or even Pulp Fiction melt your mind? When you go watch Suicide Squad: Hell to Pay, there aren't going to be in-depth introductions for every character.
It's OK to embrace your preferences. Most people like following stories from beginning to end. Now that there is 70+ years of comic history to explore, third parties have attempted ordering it all in some subjective, complicated chronology. It's not really possible, though. How do you handle flashbacks, especially when they're embedded in another story? Do you have to change the chronology to per-panel precision? What about simultaneous story releases? Alternate universes/timelines that are fully/partially "canon" and/or merged/retconned later? Varieties of characterization by multiple writers/artists?
Most of what made these superheroes "cool" in the first place was very topical. What powers do they have? What does their costume look like? Their backstories and character growth/development were fleshed out over the coming decades, more specifically in the "modern" age of comics when the demographic started transitioning to include adults.
There's no "perfect" or "definitive" sequence of events that Batman's story occurred in. That severely limits creators from writing new stories for the character without requiring hard continuity reboots. If you start solidifying that Batman grew up in X, met character Y, fought character Z, in a strict order that can't be changed, then you can't write stories that occur in between those moments. If you plan out Batman's entire chronology to fit a realistic calendar where Bane broke his back on Wednesday and the Court of Owls revealed themselves on Friday, then you (1) will find it won't make sense (because that's not how comics are made) and (2) are stripping all of the "magic" of comics away. Keep in mind: 70+ year old shared universes are an unprecedented achievement of storytelling. No other medium has accomplished something of this scale for this long. You should expect to think of something unique like that a little differently than you might be used to.
I think it's easier to get into comics when you drop the "need" to read EVERYTHING, IN ORDER. You should just read self-contained stories and treat them like separate stories. Think of it like a jigsaw picture puzzle that you're solving one piece at a time. You won't see the big picture (continuity) until you manually piece random pieces of it together over time. You even start to develop your own "methodology" (head-canon, community discussion, etc.) of putting those pieces together (reading comics) in a way that makes sense to you personally. Comics should feel more like self-discovery/exploration than procedure/work.
This is (roughly) how I got into Batman and what I suggest to new readers:
How to Get Into Comic Books (13:40) by Patrick Willems
Consider your intent/commitment. Think about stories/characters from TV, movies, games, etc. that you already like. Do you seek “good” storytelling or encyclopedic DC knowledge? Are you here to collect or read? How much time/resources are available?
Don’t try to read everything—there’s too much. Forget about continuity, universes, and timelines; it's all very confusing, even to creators/fans. Older comics can be an acquired taste for modern audiences, so first appearances/early origins may not be the best starting points. Creative teams change often, characters get re-worked, and origins are re-told (e.g. I never cared for Aquaman until Geoff Johns’ run).
Pick an interesting character/team and seek their “greatest hits”. Focus on well-received, relatively self-contained, and complete stories. You may encounter the occasional unexplained reference/character/event—just ride along (Wiki if necessary). Remember, there are so many other great characters and publishers to explore, and not all comics are about superheroes.
Comixology for digital. instocktrades for physical (US). ISBNS for price aggregate.
Modern DC characters/teams:
Alternatively, you can skip directly to the new Rebirth re-launch by reading the Rebirth event (2016) and any Rebirth #1. Check out the /r/DCcomics sidebar for more info.
Events/crossovers can be fun and/or tedious. They are most appreciated by readers already well-versed in relevant continuity. Generally, the best non-event comics integrate these seamlessly or avoid them entirely (notwithstanding editorial/executive mandates). Regardless, you may want to familiarize with major plot points.
Modern DC events/crossovers:
Discover your preferences and let them guide you. Do you like older/newer comics? Weird concepts? Super-smart meta-analysis and social commentary? Family-friendly content? Hyper-violence? Male/female protagonists? Humor? Horror? Have you noticed that a specific artist, writer, or creative team consistently produces content you like? Follow these instincts.
Suggestions to improve the guide are welcome.
Batman Incorporated is the finale to Morrison's run.
I've read a lot of Batman comics, but I can't recall much with Scarecrow in it. Jeph Loeb often includes him, the most prominent being Haunted Knight , see also The Long Halloween , Dark Victory and Hush , though his characterisation may not be perfect. Knightfall goes through all of Batman's villains, and Scarecrow has a pretty prominent presence in the story, though it's not really a Scarecrow story. Right now that's all I can think of, so I hope it helps!
As for Batman, I would recommend The Court of Owls and its sequel, The City of Owls
If you enjoyed Batman Year One, the writer behind the previously mentioned stories did his own take on the Batman origin called Zero Year that draws a lot of inspiration from Year One. It's also a two-parter. First is Secret City and it's followed by Dark City
If you want more stuff in a similar style to Year One, the same writer has probably the most famous Batman story of all time. It's called Dark Knight Returns
Finally, another essential Batman story would have to be The Long Halloween It has a sequel called Dark Victory and it has its moments but it's eerily similar to the first one and isn't nearly as good.
Personally, I would stray away from events. I'm sure some are alright but most of them just pale in comparison to what the rest of the industry has to offer.
If you have any other questions, feel free to ask.
I think your list is fine. This is what I usually recommend to new readers (and even this is doesn't feel completely right):