Thinking about Ziggurat, because I'm making an game of a vaguely similar type (action, highscore, endless hordes of enemies) and they got so many things incredibly right.
It's hard to get difficulty right in an action game. Competitive multiplayer is kind of self-balancing in some ways, your opponent sets the difficulty, but for a single-player game the designer has to set the difficulty in advance, and it's desirable to suit a wide range of different skill levels (althought not necessarily in the same mode). It's hard to get an absolute reading of how challenging things are, because your skills continuously improve as you test.
It's important to design for people less skilled than yourself if you want anyone else to play; you'll usually be the best at your own game at first. Ziggurat uses the age-old method of starting slow and ramping up gradually - in fact, it would be too gradual to be interesting once you've played a few times if not for the alien ship. (I'll get to the alien ship.)
It's also important to design for people more skilled than yourself, to make sure a game has depth and remains interesting at high levels of play. Even if nobody else ever surpasses your skills, you have your own future self to worry about - they'll be better at the game than you are now. It's unsatisfying for a game to have a skill ceiling that can be reached, after which you can simply play indefinitely until collapsed from exhaustion. It's easy enough to make something actually impossible, but that's also unsatisfying; it's uninteresting to lose only because the game threw a situation at you where you have no chance at all. Instead you must push ever closer to the limit of what's humanly possible without crossing it.
I'm thinking about endless games here. The above problems are lessened if there's an end; you can have a maximum required skill level without leaving someone stuck in an interminable game until they get bored and quit, and you can explicitly test whether that skill level is achievable. (This too is why turn-based games should rarely be endless; if at every step there's an option to keep going you'd have time to find it, and if not then you have the unsatisfying ending of reaching an impossible situation.)
So, the alien ship. It flies overhead sometime near the start of the game, and stays as long as you keep shooting it. While it's on-screen things are harder. Essentially it's a difficulty option elegantly incorporated into the single game mode: if you want things harder shoot the ship, otherwise let it pass. It's also a hint at hidden depths to the game: can you destroy the ship if you shoot it enough? Does anything special happen if you do? I haven't managed yet, and from skimming comment threads I couldn't find any indication that anybody else has, so it remains a mystery to me.
Ziggurat's score is just how many enemies you've killed. (It could measure time instead and it'd play the same, but counting kills instead of time works thematically: it's a game about vengeance, about taking down as many of them with you as you can before your inevitable demise.) I noticed some common complaints in the comments on the game, a bunch of people object to not getting score bonuses for combos, for killing lots of enemies in one explosion. But no, you shouldn't, Ziggurat gets it right. You already want to make big explosions because they're more efficient, they let you clear the screen of enemies faster. You already want to make big explosions because they go boom and the screen shakes and it's totally sweet. Awarding extra points for it would be superfluous, it wouldn't significantly change the way you play, there's no need for further incentives for something you want to do already. Those kinds of bonuses are interesting when they warp the way you play, encouraging you to take risks you wouldn't otherwise - and that's where the concept of scoring extra points for killing many enemies at once probably comes from, from a game where that was a riskier way to play, but now it's added blindly to too many games. And mechanics like that get perceived by players as a sign of added value, like they're saying "the more rules a game has the better". Sheer madness.
And yeah, the suggestion of combos has come up in the game I'm making too, and is equally inappropriate. I'm using the same scoring system of "1 point per kill" - I do like to avoid rewarding killing enemies if possible (as in Zaga-33), for the same reason as above: eliminating threats is already a beneficial activity and need not be further encouraged; but in this game some interesting play comes out of it, there can be enemies that only pose a threat if attacked, and whether to engage with them is an interesting choice; part of my version of the 'alien ship' difficulty option.
Another common complaint I saw on Ziggurat is that there's only one level (and one weapon). This is so bizarrely wrong. A small amount of good replayable content is worth much more than dozens of levels each worth playing at most once. And in Ziggurat's 'one' level there's actually a lot of content in the progression: new enemy types are introduced, difficulty rises, events happen, the background changes, the nature of the game shifts. This progression is hinted at right from the start - the sun is setting, slowly but fast enough to be perceptible, signalling that there's going to be changes to come. For me, the goal of "survive until sunset to see what happens" was a much more powerful draw to keep playing than a myriad of levels or a high score table.
It's just frustrating to see these things that I value about the game (and am trying to emulate) being perceived as negatives; its clean and pure design, the way difficulty levels and other elements are elegantly incorporated into a single level/mode. I'm not sure how common these viewpoints are in this case, a bunch of people do like Ziggurat, no idea how successful it's been. But these comments are indicative of quite common perceptions about what's valuable in a game: rule complexity is valued over depth and elegance (it tends to be mistaken for depth), quantity of content is valued over careful design and curation, graphics are valued over gameplay, and things that are the same as what people are used to are valued over anything else at all. Not everyone thinks this way, but it seems like a majority.