Look closely at the Fast Travel station in New Haven. If you pay attention to where it is located, it is outside the barriers that inhibit vehicle access to the interior of the city. Why would someone want to put that there? So in case bandits hijack the Fast Travel station, they'll pop in outside the barriers and city's defenders will have cover to gun them down.
When you open the Vault and have to fight The Destroyer, Angel only mentions that you know where to hit it to kill it, which left many players confused since there was no previous hint of its existence. However any player who payed attention to Pandora's wild life should recognize that the Destroyer has the same split jaw anatomy as the rakk hive, who in turn have their weak point on their eyes. This also means that the rakk hive might be biologically related to The Destroyer.
The fact that Commandante Steele doesn't use any Siren abilities when you finally fight her resurrected, Claptrapped self in the 4th DLC. Sirens have a mystical quality: there are only 6 of them in the universe at any given time, with a new one coming into existence whenever one of the 6 dies. It's likely Steele lost her Siren abilities when she was killed by the Destroyer, with her "place in the universe" immediately transferring to a new Siren. When you face her as Steele-Trap, her Siren tattoos are gone and have been replaced by Claptrap circuitry tattoo.
The loot dropped from the Destroyer is of lousy quality, generally no better than what would be dropped by a regular enemy. There's just a lot more of it (most of which is just ammo). This is in keeping with the Vault being full of nothing except "tentacles and disappointment".
The entire game, even series, seems to be a giant Take That! against the idea of letting corporations act in a government's place. In the first game alone you have a corporation that literally abandoned a planet of people to mutated raiders and deadly wildlife, one that didn't even try to save lives during a zombie outbreak, and one that treated its best military commander with the same respect you save for a data entry clerk. We all know what happened with the corporation shown in the 4th DLC, which, as of the second game, had waged a war with the population for 3 years, turned into a Orwellian corporation full of backstabbing corporate climbers and run by a Corrupt Corporate Executive whose policies were on par with Stalin's regime.
Why do human bosses reappear after a while? They can use the New-U stations to come back.
Related to the above; this is the first FPS universe where FPS tropes make perfect sense:
How can governments and megacorps afford to field giant armies all the time? The market only supplies that kind of resources when nobody's at war, and with the constant violence in the Borderlands-verse who has the time to actually produce anything? If there are that many guns everywhere, why are there still jerks to shoot? More Criminals Than Targets...
Answer; robots like the Claptraps keep everything running, digistruct technology makes everything literally dirt cheap, health syringes and kits keep everyone going, and the New-U stations keep bringing everyone back when they die. Thus, people have no reason not to beat each other up and/or kill each other for fun and profit because violence has no consequences anymore.
The song that plays in the end, when Guardian Angel is revealed to not quite live up to her name? "No Heaven".