Indeed, I also think one additional problem it has had is the passing of time, as in there are far superior superhero games on CoG now both released and WiP’s. Leaving the Black Magic romance shenanigans that have already been discussed ad infinitum aside for a moment, when it was released it was the best of its era, despite its heavy railroading and lack of real choices it was and remains well-written (as others have noted the spin-off is a different matter). It has since been surpassed in every possible way, I remember that as soon as Tin Star came out it began to feel really short and limited for me in comparison.
As for the genre, you can find equally well or even better written superhero genre games both released and WiP of far more variety within the brand nowadays, like the Hero Unmasked, Fallen Hero, Totem Force and for a better take on the role of the (mass) media in a superhero verse there is either @RenaB 's excellent WiP, Model Citizens: Unmasked that explores it from a non-powered mc perspective or, if and when he resumes it @ParrotWatcher’s second WiP : Countdown to World’s End, in which the mc does have powers of their own. And those are just at the top of my head, superhero seems to be one of it not the most popular genre for a reason and nearly all of them are, imho, better and more enjoyable then Heroes Rise.
The enduring popularity of HR I think did much to pave the way for all these titles and WiP’s but it has also been far surpassed by them and in that respect and in my humble opinion has not aged quite as well as some of the other Choice Games.
These days? Predominantly that it seems to have paved the way for many of those other games and WiP’s. It’'s like a teacher who has long been surpassed by their students.
I suppose Lucky was also a sweet romance that could have had potential but he was the scrappy whose development and potential plot threads were constantly ignored by his own author in favour of the far less appealing Black Magic. Really the guy only seems to have been devised to introduce some artificial tension into the Black Magic relationship and the game almost acts incredulously if you play an mc who actually chooses him because they prefer him over Black Magic.
This is true, but for me the incredibly frustrating thing is that it never seems to pursue the story elements I like most and will even discard them in favour of those I dislike.