Well, as far as I'm concerned, Maladjusted is not just the best track on the album but possibly Morrissey's best (solo) song overall. While Ammunition is the most pointless track on one of his weaker albums, and a clearer deletion candidate than "Roy's Keen" or even "Papa Jack".
But that's just to restate the opinion you already acknowledged (and most of us have conundrums like this. For me it's "Speeway" and "Reel around the Fountain"). I don't have much of interest to say about why I don't like "Ammunition", since the reason is simply that to me it doesn't contain anything that makes it worthy of note, either musically or lyrically. I can however say a great deal about why I think "Maladjusted" is a great song.
Morrissey is above all a lyricist, and at his best he is a very musical lyricist - in the way that his (oh what the hell, let's just call it) poetry occasionally interacts with the music in a way that directly strenghtens both. And Maladjusted is possibly, through his entire career, where this is the case to the greatest extent.
The melody is, as you say, repetetive. But consider it as a framework for the lyrics rather than a stand-alone element. This lyric tells the story of a life, and it does so in the rather roundabout way of jumping between a present scene loaded with desperation and longing for escape (loot wine, be mine and then let's stay out for the night etc), mood-setting descriptions (lights stretch uninviting through the night etc), significant reflections on past with no immediate context (Well, I was fifteen - where could I go? etc), reflections on present state which cut to the core (When the gulf between the things I need etc) or on the unnamed other (Still, I maintain there's nothing wrong with you etc) and finally of the resulting, call it existential, state (With a head full of dread for all I ever said etc).
And for this, the music is the perfect vehicle. It imposes a unity that is only implicitly there in the lyric. Also, it strikes just the right balance (relative to the lyrics) of constriction, desperation, defiance and beauty. In other words, it encapsulates the underlying themes of the lyric.
And it also enhances the lyrics in a more straightforward poetic way. The rigidity of the music's structure enables, maybe even forces, Morrissey to sing in much the same way as poetry is recited - notice how each line follows the same pattern of rhytm and stress. But, it is not so restrictive that it cannot be varied, and it is - and this invariably occurs whenever the focus of the lyrics shift from present to past, or from description to reflection and so on. With a more lively melody this would both have been more difficult and less effective, and again it is the steady repetetiveness of the musical structure that allows the rhytmic structure of the vocals to drive the impetus of both the song and the story the lyric tells. I'm aware that this sounds rather technical and cold, but the effect isn't. I guess the point I'm making is that it is a staggeringly well-constructed song that hugely exceeds the sum of its parts. No wait, that sounded technical and cold too. Point is.... Maladjusted is really a remarkable little piece of art that brings out some of Morrissey's greatest qualities. These words require precisely this music, and vice versa. At least it seems that way, and that's a pretty good definition of a song that works if you ask me.
cheers