To be honest there aren't many tropes that annoy me except the overplayed "reluctant hero who just wants to be normal" thing which applies to all generes when you get down to it. It's not usually the tropes that are bad, but the way they are done. Mostly when I wind up rolling my eyes is when they use a trope ham handedly and I've seen the same basic thing handled much better in other productions.. or worse yet it just generally does not fit.
I'll also say that don't confuse a bad trope with audience projection. I notice people talking about things like "a lack of female scientists" and the like. To be honest unless your dealing with insane levels of political correctness not all groups are going to be evenly divided right down the middle. In most shows just because you don't see any female scientists in a particular group, or on a particular project, doesn't mean that this is indicative of the society as a whole. What's more I'd say that I've found the case to be the opposite if you want to really go for the PC aspects of things, where it's usually the female characters that are given the more cereberal roles, while the guys tend to do the hands on action. Being the scientist, hacker, engineer, etc... is the quintessential way they work female characters into shows. For example in Star Trek you'll notice Janeway and Dax were both science officers, the only time we really saw a straightforward "action girl" (although Terry Farrel stepped up for it a bit as Dax) in Trek was when we had Tasha Yar in security, but she was removed from the show pretty early on. While you DO see action girls in science fiction, more than enough where I don't think it's a problem (Gina Torres and Summer Glau in Firefly come to mind for example, as does Starbuck in Battlestar Galactica... to say nothing of Number Six, as Tricia Helfer seemed to kick people's butt quite a few times even if she was a bad guy... then of course we've got Beka and Rommy in Andromeda, and others). Overall it seems like there is a lot of parity overall here within this genere, but if anything you'd probably make a better case by saying there are too many girls in support roles while the guys do all the cool fighting stuff. The point here is pretty much that you need to be careful not to project issues onto things that aren't really there.
It's also important to note that when it comes to TV and movies backstory isn't always spelled out implicitly when it's not entirely needed. In most science fiction, though not all of it, there is usually some kind of huge apocalypse that took place in the past that caused humanity to unite. Typically the surviving group or the one that pulls everyone together is whatever nation or culture the writer happens to be from, usually the US or Europe, though given the power of the western world a lot of other countries ALSO tend to set the biggest surviving group here. As a result the majority of people being white makes a degree of sense in a lot of these concepts. In some visions of the future where civilization never faced an apocalypse things might be different, as they would be if another part of the world was where humanity rebuild from. That said the odds of seeing a perfectly politically correct representation in any given group of people are minimal. What's more if your dealing with a future that is hardly utopian and there is still a lot of crime, gangs, or even more than one nation/culture surviving, your still going to see people ganging up with people a lot like them, as a result if your doing a show for a western audience, your largely going to be focusing on a ship
with westerners and that morality, even if others technically exist.
When it comes to cybernetics, genetic enhancements, and similar things there is the very real cost of special FX, especially if you want it to look good, and your doing it with a main character that is going to be there all the time. Every time someone fired off a phaser in say "Star Trek" cost a bundle of money to make it look right apparently, so as a result you didn't see gunfights in every episode, and even in the more action-oriented "original series" it tend to ultimately come down to fisticuffs because at the end of the day that was cheap. Needless to say with concerns like this, having some dude run around as an overt cyborg in every episode is going to be a pain. With genetic enhancements things get even more complicated, because for one you want the audience to empathize with the characters and the world, and really if you follow that through to the point where everyone is superhuman... well things get wonky really quick since to make any plots at all you have to start working on a level so far above the audience that a lot of them won't "get it". Not to mention issues like in a show where everyone now has night vision genetically built into their eyes, why would anyone carry a flashlight, or why would they even bother to light rooms... other than for the convenience of the audience watching things. Not to mention the whole ethical debate in genetics, where as technology advances your rapidly going to wind up with a lot of people that are simply better than other people around at the same time. Technology not always being backwards compatible. As a result let's say you make "Humanity 2.0" that's great, let's say you deal with the whole issue of upgrading everyone or otherwise keeping society working until all the regular humans peacefully pass on and the genetically enhanced are now the standard, what happens when Humanity 2.1 comes along, and it's not backwards compatible with 2.0? Worse yet what happens when we get to humanity 3.0 but it's very resource intensive so of course only the richest people can afford to become 3.0 or have their children enhanced that way? Forget regular racism... in this case it would become a scientifically undisputable fact, people are only as good as the technology intergrated into them on a fundamental cellular level. The higher the generation of technology the faster, stronger, and more mentally apt the person gets. Sure regular "Human 2.0" might be superior to the norm now, but when he's compared to say a human 5.0 he's little more than a retarded child in comparison. Not to mention ongoing dynasties where of course those who adopt higher genetic technology first thus exploit it to ensure they always have the best enhancements to they and their children stay on top... one could always say "well, at a certain point you could stop technological development here" but really once you let this cat out of the bag, it's never going to stop, it just means your going to wind up with people becoming more advanced on the black market... and of course inevitably start some kind of eugenics war.
Trek didn't go into the whole "genetics" thing in detail, rather it not only had an apocalypse which humanity rose out of by the US using facit military units controlled by drugs (Encounter At Farpoint) which pretty much conquered the remnants of humanity into an empire. The empire which was then threatened by the creation of genetic supermen like Khan who being better than everyone else started to take over and needed to be stopped. The implication being that there were some glitches in the original technology that made the supermen go insane (to an extent), but some extended information on the subject made Khan a little more sympathetic, as a big part of it was also human paranoia and fear over the future. This issue came up again later in "Deep Space 9" where Julian is revealed to be genetically enhanced and it's shown that there is huge bigotry against those who have been enhanced, they are not allowed to do anything of worth as a general rule, largely BECAUSE they are so much better at it than normal people. He winds up managing to wrangle an exception and stay in Star Fleet (and being allowed to practice medicine) but it more or less covered exactly why you don't see all the humans running around with enhancements in Star Trek. Something which incidently also makes them kind of stupid when you then look at the beating humanity winds up taking at the hands of genetic super soldiers in the hands of the Dominion (but that train of thought is never fairly brought up). The point is Trek covered this.
Andromeda, another thing coming from Roddenberry's writings had a more mixed message. One of the primary bad guy factions are a group of genetically enhanced supermen, who themselves bring down the original interstellar government. Albeit there were other extenuating circumstances (The Vedrans, who were the driving force behind it rather than humanity had disappeared and sacrificed themselves and their system to basically create a giant trap for what amounts to The Devil unknown to everyone else), along with a message about the failures of being too moral, as Dylan had the opportunity to stop the entire thing from happening, but he didn't because he didn't think the government could fall at the time and didn't want to sacrifice civilians. He went back in time early on to that choice and more or less admitted he did the wrong thing if I remember, but ultimately had to live with it. HOWEVER in addition to this group of bad guys you had another group of bad guys who were all about "genetic purity". The main character himself being a human hybrid, one of his parents being a genetically enhanced "heavy worlder" (designed to live on planets with higher than normal gravity) which gave him superhuman strength and was the justification for some of his crazier fighting stunts and why he could handle genetically enhanced opponents and very nasty aliens in hand to hand combat for the most part. It was a lot more balanced on the whole issue overall than Trek was.
