This is the storyline that led many fans to call Tony Stark 'Der Eisenfuhrer'.
The Marvel brass really regretted not giving the Thor clone an official name right away, since the fans' decision to label it "Clor" seemed to irk them. Marvel later on named it "Ragnarok." Fans still call it Clor.
Flip-Flop of God: Nobody seems to be able to agree on exactly what the Superhero Registration Act is supposed to do or say.
Follow the Leader: The scene where Sally Floyd breaks Captain America by asking him about American pop culture has been compared with a similar scene from the Green Lantern / Green Arrow comic book of the '70s.
Civil War was written in the aftermath of 9/11, the reaction of the Bush administration, and the "War on terror". Also MySpace.
The politics dealt with in the event have also not aged well. The frequent allusions to the Pro-Reg side operating more like police officers is especially cringe-inducing, since later controversies in the mid-2010's have led to the US police being heavily scrutinized and painted in a negative light by various sectors of the public.
What Could Have Been: Mark Millar and Brian Hitch were working on a story for The Ultimates called Civil War. Then Millar got the chance to write Marvel's crisis crossover of the year, so he declined that project, and adapted some of his ideas to the main comic book we have read. This pretty much explains the common criticism for the storyline that accused Millar of writing Ultimate Cap instead of 616 Cap.
The story was originally going to end with the civilians that tackled Cap to give both sides a What the Hell, Hero? talk. Realizing the conflict was pointless, both sides would enter a temporary truce to clean up the mess and the new status quo would've likely had Cap still at large leading the Secret Avengers. The plan was changed to what we got due to the apparent intervention of Joss Whedon, who suggested that one side had to win after everything that had happened.
Annotations on the book's script states that Namor came to Cap's aid out of nostalgia for their old partnership back in WWII. This conflicts with tie-ins explaining that Namor only had interest in the conflict due to his cousin Namorita's death.
In what was possibly an attempt to counter the criticisms explained in What Could Have Been, Marvel claimed the difference between Ultimate!Cap and 616!Cap was that Ultimate would've gone along with Registration.