I don't suspect I'm alone in thinking that TDKR is a bit of a mess while still having some good or even great moments. But it's interesting that some of your criticisms of DDS2 could easily be turned around onto Rises.
You're not alone in that opinion certainly but whatever the flaws of TDKR, DD season 2 has much more blatant and worse examples.
Arcs not feeding into one another meaningfully? Well the Gordon letter stuff doesn't really come to much of anything now does it? Bane revels it and it changes... Nothing.
It's how Bane gets the truth about Harvey Dent out in the open and gets the blackgate prisoners on his side. It's hardly comparable to Frank and Elektra's story arcs basically existing in different universes with Matt himself being bounced between unrelated story arcs like a pinball.
Characterization about a code against killing being hazy and inconsistent?
Batman just tells her to guard the doors, not to actually shoot anyone. In contrast, Daredevil is starkly opposed to Frank killing people to the point of even debating it but at the boat, He out of nowhere says "Let's try it your way just this once", How in heaven's name is that better? Worse still, Matt says he and Elektra can't be together because their just not right for each other but then at the end, He wants to run away with her?
The supposed commentary of Bane's "revolution" is muddled at best and we never get any idea about the people of Gotham's reaction to it. The idea that Bane allowed the police to be cared for instead of just gassing them all to death is only out shined in incredulousness than the idea that said same police officers would after being trapped for months and fed the bare minimum underground would be somehow an effective fighting force. Let's not even begin to get into why Bruce Wayne would be okay with the inherent danger of a nuclear fusion lab being within Gotham City limits.
The whole point of the revolution is to tear Gotham apart while forcing Bruce Wayne to watch, experiencing the depths of his failure in trying to make Gotham a better place. It was a missed opportunity to show more citizen reactions but I felt the former was communicated very effectively. It's still a far better plot than whatever the Hand was trying to do. The whole part of the Gotham police being able to fight after months under ground also requires some suspension but honestly no more so than a man being able to get up and function with half his face burned off like TDK. You're really stretching for the last one.
Way more so than in DD Season 2 which I honestly don't find any great level of fault with and think executes it's stories and character arcs to a more consistent and satisfying end.
Not even close. The main problem with the second season of Daredevil was that it succumbed to IM2 syndrome, in that it became more focused on setting things up for other shows rather than focus on it's own story. TDKR at least gave a Bruce a satisfying consistent character arc, what exactly was Matt's? His purpose in that season was mainly to serve Elektra and Frank's character arcs and even those were muddled. The decision to add a conspiracy angle to the death of Frank's family was ill-advised and revealing Elektra as the Black Sky while giving us no clue of what exactly that actually means was ridiculous.
In terms of consistency, DD season 2 has way more problems, especially in regard to the Hand and their lack of clear motivation and no storyline was really brought to an end there, They all just kind of fizzled out.