I'm a huge comic book collector and fan so I shall be your resident smug douche bag for the evening; if you've any further questions just ask. Keep in mind though, I've been awake for over 24 hours so you're going to see some crazy ramblings, so strap in.
Firstly, your comments regarding characters coming back from the Dead; This criticism applies purely to Marvel and DC superhero comics (However the "Big Two" comprise quite literally 70% of all comic books sold and are the only companies that can afford to advertise in any capacity at all, including to actual comic book readers, so when people make this assumption it's more than understandable), although this problem is about as bad as you've heard, although it applies ALMOST exclusively to the main character (or main cast in the case of a team book) and to villains. If you read something from other publishers you're not really going to run into this problem anywhere near as much (unless it was actually part of the plot, like how in a movie you'll see a character fall to death in the 2nd act and then come back to save the main character in the climax of the film).
Secondly, your complaint about having trouble discerning whether or not something is canon/non-canon/alternate universe tells me that you've not really tried to read comics outside of maybe grabbing a single book, reading it and then calling it a day (which is fine, that's how a NORMAL and SANE person would test a product). The whole continuity/alternate dimensions shenanigans is blown out of proportions a lot by comic book readers who are trying to make what is considered by many to be a niche hobby (comics are hardly niche, people may rarely buy the monthly books but TPB sales are quite large, even after the 2006/2007 comics crash, yes comics had a crash, even before the recession which only made things worse) sound really impressive, deep, complex and impressive when it really isn't. Since your statements make it clear you're essentially referring purely to "mainstream" superhero comics then I'll do a brief commentary on that:
Marvel comic book continuity makes it so that everything that's been written has happened and is in continuity. If you want to know how comic continuity works think of it like LOST, except with all the revelations making sense (well, with the rare exception). Think of it like a serialized drama that has now reached its 30th season.
DC continuity is essentially the same although on very rare occasion (years, even decades apart) they'll write a story where reality is re-written or something which changes the past or something like that. If they don't tell you in the story what has changed then you're not meant to know for a while and it will play out in future stories and you're meant to witness for yourself the differences.
Even under these circumstances that means you might just want to read a character that hasn't been around for 30+ years and if you do it all depends on the character and/or series, some series will go on for years/decades and never have any continuity problems that require something crazy to happen.
Thirdly, there's no real way to get alternate universes confused. There's rarely stories told in alternate universes and the few that are told get mini-series (between 4 to 12 issues in length, have a beginning, middle and end, they're not open ended) and these series will more often than not say in a blurb at the start of the story that they're an alternate universe story (and on the back cover if you're reading the TPB/collected edition). They also get special names, like "Superman: Red Son" and if there's an actual sequel (a sequel to this sort of story is rare to the point of hilarity) it will have a naming convention so that potential readers know its a sequel (as well as info on the back/inside saying that it's a sequel), like Marvel's Earth X Trilogy (Earth X, Universe X and Paradise X respectively). DC even puts a giant logo on their alternate universe books to tell readers that they're set in an alternate universe in addition to the blurbs/names.
Have alternate Universes ever had their own continuity with multiple books? Yeah, but they would become part of an "imprint" and they're set apart and named specifically to avoid this sort of confusion, I'll give some real examples:
Marvel 2099 - All the books were set in the year 2099 and every title related to the imprint had 2099 in the title and a giant logo in the corner that said "2099", like "Spider-Man 2099"
Ultimate Marvel - All books had "Ultimate" in the title (eg. Ultimate Spider-Man) until a relaunch where all books had "Ultimate Comics" in the title (eg. Ultimate Comics Spider-Man). Yes, this was a really stupid name change.
MC2 (Marvel) - Set 15 years in the future from a specific point, all books had a giant logo on them that said "MC2".
DC - Has a current ongoing series set in an alternate universe on an alternate Earth, the Book is called Earth 2, it's in the fucking name.
I know people find this daunting despite really being interested and liking the characters (like the OP), but there's no reason to be, it's just been built up by readers to try and make it all seem more impressive.
Finally, comparing most manga and superhero comics doesn't work at all, most manga isn't never ending nor is it intended to be, superhero comics are intended to be that way and have been going on for longer than most current ongoing manga. Comparing non-ongoing manga to non-ongoing, stand alone comic series however is reasonable enough though. There is one section where manga ongoings win hands down though, they don't fuck with the numbering because they're not fucking idiots. You hear me Yankie comic companies? Cut it the fuck out.
The Wykydtron said:
I can't stand going into a story anywhere but from the start. Hence Western comics are a bit of a nightmare to me. The prevalent font style gets on my nerves too. You know the bold on every other fucking word? I hate that. Small example I came up with.
"Hey Iron Man do want a coffee? It's been ages since my last drink"
Argh, it breaks the pacing instantly, like every bold word acts as a new sentence for me, similar to When People Do This Shit It Is Annoying. I suppose the bold is for speed reading? I do have a quick reading speed but the bold serves to piledrive it into the ground for me.
I also like the way manga is black and white, it looks clean and easy to follow. Sometimes western comics are a complete clusterfuck of colours and I have no idea where to follow the panels.
Y'know when you have to chain four arrows towards panels just to show us where to read, it's kind of bad design.
The font complaint. This. This is so god damn mother fucking true.
If the colors are making it hard to see then that just means you've got a gibbering retard for a colorist and even then you shouldn't notice that unless something truly insane is happening on the page or they only got the job by diddling the boss. When color is used effectively though I'd say that it's completely superior. I'd also say that terrible panel layout is hardly unique to comics, god knows I've read enough manga with this problem, although colors only make this problem more confusing.