I've had the same exact problems. It's often difficult to see what your game needs, or what's wrong with it, and you find yourself banging your head against the wall trying to figure it out.
I'll see if I can help those head juices flow...
In it's current state, I think the strongest element your game has right now is the background stories, namely for the antagonists, as they are the most interesting.
If you want to add some element of satire, I'd say you take the name "Night Knight" and thematically add any comical element that has to due with "bedtime" to his persona. All the stereotypical kid stuff like blankets, pajamas, teddy bears, night lights. Make him sort of a dufus. Maybe he sort of "thinks" he has "superpowers", but doesn't, resulting him to be laughed at and not taken seriously by his foes, sort of the underdog effect. Maybe no one takes him seriously, and he has to prove himself. I know it's been done a lot, but cliches are okay sometimes. They're even better if you're poking fun at them. That's why spaceballs was so funny.
Another route would be adding some kind of animal theme to his character. A lot of comic books do this because it's so easy. To apply animal behavior to something is so easy, it just comes natural to little kids (they pretend to be animals all the time). You could take a variety of nocturnal animals and apply their associated "powers" to Night Knight. Bats have echolocation, possums can hang from their tails, skunks, well, yeah. Heh, even owls can eat
whole flipping mice and puke up their flipping bones - but I digress.
Why do I suggest this? Because even though Night Knight is a very interesting character, his gameplay mechanics need a little
something, it needs that special kind of hook. You can easily add some "Power" or even some "Quirk" to his character and reflect it in the gameplay. If you look at most successful games they have that little gameplay element that no other game has, or they take an existing element and make it better than anything previously delivered. Even if it isn't new, it needs to
feel new. What can Night Knight do that no-one else can? What can he do
better than anyone else?
Night Knight's current background story is quite tragic, and is probably inspired by Batman's background, I imagine. Batman takes the element of tragedy, and makes a stone-cold, gritty, and dark universe. Well, at least that's the story now, it wasn't so in the 60's. I haven't played the "Arkham Asylum" series but I can tell from footage that played heavily on that dark grittiness (and did so very well I presume). And that grittiness was probably reflected in the gameplay.
You already have some neat mechanics, I especially like the hologram ability. The moon shards are neat too, but at first glance I can't really tell what they are. They would be the first thing I would try to improve on, as they seem to be your core mechanic. It's really hard for me to say, as I really don't know how it feels without playing it. I'm usually dry on ideas in this department when it comes to my projects, which is often why they get pushed under the rug. I have the personal novelty of "bringing life" to a character, but when that wears off, you have well, a guy that can walk and jump.
I'd recommend reading
The Art of Game Design: A book of lenses not because it will make you the perfect designer (no book can do that), but because it does have a lot of useful information. I've just finished it myself and learned a lot of neat stuff. Alternately you could use the
Deck of lenses to "debug" your design, and to see
where you should start improving your design.
I'm sorry if this post got a bit rambly or incoherent. I hope it could at least be a little bit of help, especially since I often feel your pain.