The anime of Deadman Wonderland did quite poorly commercially in Japan, so it was not picked up for a second season. Basically there's no hope in hell of ever seeing him get out of that prison, although you could read the source material instead.
Those drawn-out things like you describe tend to be confined to stuff based on shonen battle mangas. Those mangas are released at maybe 24 pages per week, and they need to keep the young teenage readers "hooked" week after week with ongoing action, and with a younger target readership, you need to compensate for having many readers who just cannot go back and start at the start, these comics need to be able to be picked up in the middle with no problems. So you have to make every 24 page installment exciting, have cliffhangers, and make sure you can pick up and drop the series at any point without getting too confused about who is doing what. These constraints don't really allow the writer to have tons of intricate long-term plots going on. Really you would only have space for 1-2 side plots along the main plot at a time. Plus of course the writer doesn't want to wrap up a popular series too soon, so you draw out the main battles, have lots of side quests/smaller battles, and you drop miscellaneous plot elements quickly if they get in the way of telling an exciting tale in each 24 page installment.
Light novel based series *can* do things a lot different to mangas. They're usually released in tankoubon format (though some are serialized as written chapters in magazines), which is about 200 pages of written material, so they can have a big action start, slow down in the middle and get more "talky" then back to action for the finale of the novel. But a big stretch of discussion in the middle of a manga would totally kill your readership. For light-novel based anime you get arcs somewhere between a couple of episode to a season with a well-defined story arc, and intricate plotting. The only caveat is that these types of anime tend to feel like they "reset" a bit after each arc, since the start of each novel will have the characters in their daily life, then Adventure Happens, and it's resolved maybe a little too neatly. The Index / Railgun series and the one about vampires Strike The Blood are good examples of this type of series, each of those has arcs which are 4 episode each, corresponding to a different novel in their series.
I really never got into shonen battle stuff at all. I'm getting into some shonen sports series now. In sports series, the overall arc tends to be based around some real-life tournament, so there's a definite time limit on the future action, and many of them are based around school team sports, so after that tournament is over, some of the characters will have to graduate. Usually the main characters are first years (three year high school) and the overall story focuses on their single year of tournaments. They don't usually go past this, as then you'd just be explaining the same tournaments over again, which is not fun for the writer or reader. The way these mangas extend the lifetime of the series is not by tacking stuff on after the final battle, they do it through flashbacks, backstory and character development. So you end up with detailed character histories of not only the main characters but most of their opponents as well, and it's very rare that they will try and depict the other team as pure frothing evil. My favorites in sports: Hajime no Ippo, Yowamushi Pedal, Kuroko's Basketball and Baby Steps.