i'd seen that list a long time ago, and afair agreed with some, disagreed with others. it should be noted, too, that there's a rating system there to designate ideas which could be expanded up to 'don't even try, you hack.' i don't see quite as much cynicism here considering the list is accompanied by at least a slight justification system.
the one i'd add to the list (maybe it's there and i just don't remember) is how the special forklift, or some piece of equipment, in chapter two shows up again at the end to battle the bad guy. i like to reference the awful movie 'the core' here: there's one point where an engineer is talking about what happens to the ship if trouble occurs, what to do, and gives a warning, if i remember correctly. lo and behold, it happens. it's just obvious foreshadowing.
what can be done that's not been done a million times as far as i know? well, parody springs to mind, but even that you've got to be careful because it's got it's own cliches, too. we see some cross-genre stuff, like sci-fi romance and sci-fi horror/mystery/suspense. i myself don't know how many times i've started the same fantasy detective story. for fun, i used to do short SW fanfic as in those time-life books formats that was supposed to be a review of urban legends in the SW universe. basically, a lot of it was a lot of retooled stories based on the legend of 'the black aggie' and stuff.
i think you find a lot of great stories being retold in various genres, too. well, maybe not so great all the time, lol, but there sure seems to be a ton of king arthur in space-type stuff i've read. don't bother retelling 'the magnificent seven' in space, it's been done already, and in movie form.
the last sci-fi i was working on had a colony on a remote planet who, over the years, developed its own lifestyle and culture. they just really wanted to keep things the way they were, and since they were assumed to have been lost in action as far as earth was concerned, keeping their colony as low-key as possible was of paramount importance. though a series of events, a young man's work bot that he refitted to be a sex bot goes a little haywire and sends a message to earth for help. it's the boy's fault, of course, so he has to retrieve the electronic message. it's a weird universe full of weird sh!t, though, so as the young man gets close to catching the message, it's been filtered through so much alien technology that it develops a sentience of its own. and quite a nasty little attitude, too. well, so would you if someone was trying to essentially kill you.
the boy goes through a ton of wild adventures, which i tried to make as comical as possible with, indeed, an eye out for cliche and plenty of nods towards them. during his adventures, he's destroyed, rebuilt as a woman, loses everything he holds dear, grows up, etc.. inspired by an episode of 'red dwarf' and the sea of the dead in 'titanic', my hero finally cons the amazon-like warrior women (oh, big-time cliche) into taking him to the 'dead zone' where billions of bodies float in space. he has to find his cloned male body (the one he starts the adventure with, not the one he had tweaked and worked on) and take it back to the crazy scientist living alone with his daughter on a space station (another cliche).
at one point, the guy pissses a race off who then vow to launch an assault on the earth capitol in texas (another one-world gov't cliche). he's unable to stop them, but it doesn't matter as the invasion force, we find out, is practically microscopic (how many cliches am i up to?) and is literally swatted into defeat, culminating in the reporter's newscast where she's saying, 'an invasion force attacked the capitol today, causing hundreds of dollars of damage and irritating dozens of people with tiny laser beams....' (as an aside, this is one of those rare stories where i do happen to delve consciously into themes before writing away.)
my point is there's no way i could tell this story without cliches. it's sometimes in how you tell it. sometimes it's a crutch, and you usually wind-up with a pretty blasse read when that happens.