These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Alternative Character Interpretation: Gordon Rennie in one of his monthly rant columns in the Judge Dredd Megazine speculated that there is much Ho Yay between Johnny and Wulf. Naturally, this has resulted in much Internet Backlash and even prompted John Wagner to specifically write a scene where Wulf gets laid just to debunk this.
Anvilicious: Early strips were pretty heavy-handed with the anti-mutant racism.
Replacement Scrappy: Feral falls squarely into this in the SpinoffStrontium Dogs; he wasn't necessarily seen as a bad or hated character, but since he was filling in for the lead after Johnny Alpha had died, he had very big shoes to fill.
The Woobie: Johnny is a rare example of a manly character who still manages to fall under this trope. Whether it's the sheer amount of crap that gets piled onto him, or the way he stoically accepts the abuse and soldiers on; if you don't occasionally feel the urge to buy the poor man a beer and pat him on the back, you have no heart.