The Other Major Cliches to Be Wary Of

It's little question that you're likely to deal with the thornier issues morality, magic, and chaos. There are some interesting issues that may make those topics a little easier to deal with.

Good vs. Evil

There are three potential issues; in essence, the issues are concerned with the perception of good and evil more than the conflict itself. Good vs. Evil is a solid conflict; it's just the details that may be problematic.

First is that there may be the cliche misdirect: Who you introduce as the bad guy and good guy are actually the good guy and bad guy. respectively. Unless this is handled just right it's either obvious from the get-go, or it feel like a betrayal. I appreciate the temptation: It's either a way to keep things fresh, or to show that good vs. evil depends on perspective. However, unless it's handled correctly, it can come off as a cheap twist; that is, it was done just for keeping the readers off-balance more than anything interesting. So seriously debate using it.

The second is that you may feel like making the good guys corrupt and the bad guys downright nice in order to show that there are many shades of gray and is a good indicator that the world is dark and gritty. I'm not saying that I don't disagree with that style of writing; the flawed hero and honorable bad guy are definitely important archetypes and there's nothing wrong with it if it's done right. However, be advised that it's a sign of amateur writing: It's an easy way to ratchet up tension (we don't know who's capable of what) and being edgy just for the sake of being edgy is more annoying than anything else. So make sure you're using for an actual reason and you should be okay.

The third is the worst of all: That anything is good given the right context. The problem is two-fold: First, you need to keep in mind that, as a race advances certain things are left behind; murder and rape are arguably the two best examples of that. Aa a corollary, you can't judge a race's morals by what it becomes; in other words, there has to be a point where a reasonably peaceful race can no longer be judged by the crimes it committed centuries before. People have to have a chance at redemption: Their sins need to be forgiven but not forgotten if they are going to advance as moral creatures.

This can be applied to a race as a whole, in that a society forever judged by the actions of those in the past can never truly advance. This can also lead to racism (if the group is never given a chance to prove itself then it's permanently relegated to second-class status) and other societal problems. However, the whole "evil race" concept is just not palatable by modern readers, especially as we've seen the perspective shift for numerous groups (such as the Germans and Japanese) from an evil group to the best of allies. If you need an evil race, then it's time to question how good your writing is. After all, if people can change and be respected for it, shouldn't that apply to cultures as well?

The other aspect to this is to not judge a past culture by modern rules. It's just that the rules of living were vastly different then, and solutions that we would not find acceptable today were common even a few decades ago. That is, it's assumed we've gotten better as a species and so it feels wrong to judge past societies by how they lived back then, especially as the advancement in morals were due to the evolution of philosophy and technology; the rules were just different back then due to a number of issues that just didn't apply back then.

Magic

This needs to be defined rather tightly as quickly as possible. Stories in which magic is defined or limited tend to be better than those where magic can do anything. You just can't provide any actual sense of suspense when it's entirely possible for someone to use some magic to get out of any situation. It also means that the characters will have to think their way through. At the same time, avoid elemental magic just for cliche issues.

This is not to say that a soft magic system can't work. It just needs to be defined well enough that it's not a deus ex machina; if it's defined too loosely, then mages become far too powerful. Sure, mages should gain a certain amount of power from people not knowing what they are capable of, but if they are capable of too much then they become too powerful, and that's not a good thing for your story. If you do make them too powerful, then make sure that you have some way of balancing them out, such as rarity, some particular creature that hunts mages, or an element that can be fashioned into a weapon against them; if a weakness doesn't exist naturally, then something can evolve that can serve that purpose.

Magic can be a great tool provided you allow for its effects on the world.

Chaos

When used right, true chaos is neither evil nor silly. This isn't to say that it's always a good thing; it just is. Chaos should foment change, growth, and allow for some reflection. At the same time, it can damage organizations that are too calcified, cause too much growth, and get caught in its own distractions. You see far too much of the latter three, and not nearly enough of the former three as writers forget that Chaos has its good side and focus too much on how it disrupts society. More people need to read "Monkey (Journey Into The West)"; Chaos is more than a disrupting force, but when used correctly becomes part of the balance of a world, allowing the world to run better than if it were run by Pure Law: You need those bits of randomness to keep the world chugging ahead rather than frozen in place, and there should always be an exception or loophole to a supposed unbreakable law that can be exploited.

I really wish people would remember that sometimes you need a bit of randomness; too many heroes get too angsty because they forget that there is more to life than just the usual scheduled battle; the little random bits, such as a beautiful smile after a hard battle, a rainbow behind a cloud,, and gentle rain after a heat wave, color life and make their lives enjoyable. They also provide a welcome break from the action and 

 This should be enough to fire you up. Good writing!