Maybe Audrey II isn't evil, maybe it's jealous of Seymour's relationship with Audrey and resolves to keep him all to itself.
Seymour himself. Is he a passive little wiener whose tragic flaw is a spineless inability to stand up to anyone, or was he always selfish and amoral but just didn't have the resources to make anything of it?
Mushnik. He took in a street kid and is concerned for Audrey when she shows up with a bruise, but he jumps at the chance to take advantage of Seymour once he starts becoming successful and doesn't hesitate to try to blackmail him about Orin's death; was it mundane greed, or was Audrey II manipulating him in order to push Seymour?
Foreshadowing: Audrey II sings "I swear on all my spores/When [Mushnik]'s gone the world will be yours." This is the only reference to the plant's spores, and later on, we learn that Audrey II reproduces through fragmentation. And around that time we also learn that Audrey II's promise was empty: a promise it made on something it doesn't have.
I Liked It Better When It Sucked: In 2003, a broadway production of this opened, which starred Hunter Foster as Seymour, had a much bigger budget and a more elaborate stage set, with a full orchestra. This was not reacted to warmly by people and was deemed a bastardization; the morals were gone and replaced with a more Disney-esque feel, and the strings and shimmery chimes seemed to get in the way of the rock feel the tracks had. Furthermore the actors didn't fit, and at times were obnoxious, and people were more partial to minimalist stage sets as used in school productions and even the off-broadway production, which seemed to make it more "warm" and intimate to the audience; this production closed down less than a year later due to poor reaction. It wasn't all bad though; the cast recording was often a big seller because it included demos of excised songs from the original production (Bad, The Worse He Treats Me, We'll Have Tomorrow, A Little Dental Music) sung by Howard Ashman, and still continues to sell today for such a reason.
Jerkass Woobie: Seymour. He definitely crossed the Moral Event Horizon at some point (where exactly the point was is up to you), but when Audrey dies and he's left all alone, you have to feel a bit sorry for him. His backstory (a poor orphan taken in by someone who doesn't even like him), and his desperate pining for Audrey at the start of the show, watching the girl he loves get abused by someone who doesn't love her the way she deserves, garners a bit of sympathy, too.
Audrey II eating Audrey. Some blame for it rests on Seymour as well.
Seymour killing Mushnik. Scrivello deserved what he got, but Mushnik was killed purely so Seymour could save his own ass.
Orin Scrivello, meanwhile, crossed it long before the show began, what with the way he treats his patients. Not to mention poor Audrey.
The Woobie: Audrey (the human). Her father ran out on her when she was a child, and she grew up poor, which is why she's trapped on SkidRow. She has absolutely zero self-esteem, which is why she stays with her abusive boyfriend while secretly pining for her sweet coworker that actually treats her well — not only does Audrey not know Seymour loves her back,she doesn't even think she's good enough for him. When her scumbag boyfriend gets eaten, she's understandably glad he's gone, but feels guilty for feeling that way, in spite of how terribly he treated her. Oh, and Audrey II eats her for no goddamn reason other than to mess with Seymour.
X Meets Y: Little Shop is best summed up as Edgar Allen Poe meets a Disney musical. Which makes sense, considering Alan Menken and Howard Ashman did the score.
Adaptation Displacement: Fans of this movie are not aware of the Roger Corman movie it was based on, and are disappointed when they rent or download the original, and find out which one they're watching. To an arguably lesser extent, it has displaced the stage musical. See above for the original film's adaptation of the book.
Alternate Character Interpretation: Seymour Krelbourn. Is his letting Orin suffocate from laughing gas revenge, or is it due to him being in shock? Is him letting Mushnik being eaten by the plant because Seymour forced him to walk into the plant, or was Mushnik's backing up into the plant's mouth an action on his own accord?
The movie actually encourages this, as unlike the musical Seymour is never shown actually enjoying his new-found success built on the bodies of Audrey II's victims. This is likely a big reason why the ending had to be changed.
Ending Fatigue: As faithful as the original ending was to the stage musical, it drags. The ending consists of two long musical numbers back to back, the first with Seymour getting eaten by Audrey 2 and the second consists of Audrey 2's army destroying the world. The sheer length of it all may have contributed to test audiences being turned off.
Shortly after the Blu-Ray release, a new, full-color workprint surfaced, claiming to be the final cut shown to test audiences and showing an alternate cut of the ending which is much shorter. However, it eliminates the feeling that The Fourth Wall Will Not Protect You by cutting out the plant attacking the audience.
The original ending wasn't that faithful to the play to begin with. "Mean Green Mother" wasn't included in the play version, and Seymour willingly fed himself to the plant to try and destroy it from the inside. Moreover, the original "Don't Feed the Plants" sequence is 3 minutes long in the play, whereas the final cut adds 4 more minutes of instrumental song with footage of people running away.
Special Effects Failure: In a movie with such good special effects, its one notable flaw stands out; during the scene where Seymour electrocutes the plant, a digitally added explosion is placed over it and the plant simply disappears.
Uncanny Valley: Deliberately done with Christopher Guest. Frank Oz kept telling him to be more and more excited by the plant until he was basically a robot.
Visual Effects of Awesome: The Audrey II puppet is possibly one of the most complex animatronics of its kind, and still holds up to this day. Frank Oz wanted to direct this film for a reason!
There's also the take over scene in the original ending. All of that was miniatures and puppets!
It gets even more impressive when you learn the puppet wasn't able to move nearly as fast as we see in the film, requiring all those scenes to be shot with Rick Moranis performing at half-speed.
The giant Audrey II sequence was so well-done that master puppeteer Frank Oz still doesn't know quite how he was able to pull it off to this day.
Peter Wallach's stop motion animation is pretty good as well.
What Do You Mean, It's Not for Kids?: Through the haze of the years, it's easy to think this movie as a little less grim than it actually is - you remember the songs (composed by Howard Ashman and Alan Menkin to boot...yes the same duo who wrote many of the classic Disney songs from the Disney Renaissance of the late 80's and early 90's also created the musical about a giant scary plant that eats people and manipulates people into doing the dirty work for him) and the jokes, and the fact that the ending is happy. But parents who haven't watched the movie recently should beware:
If your child is afraid of the dentist, you may want to skip that part.
The scene where Seymour chops up Orin and feeds him to the plant, which laughs with its mouth full of Orin...
That scene actually could've been worse, as props of Orin's head and arms were crafted. Oz decided at the last minute that it was too gruesome and had the props wrapped in red-splattered newspaper for the scene to obscure them.
We actually see the plant swallow Mr. Mushnik whole and later attempt to do so with Audrey.
This applies even moreso to the play, where the protagonist actually murders multiple people, all of the main characters die at the end, and the world ends.