For starters, the game must be winnable by all factions, even if the odds are against that happening.
If there is a large faction (the town/innocent team) which has two protector/doctor/defender roles, then it is entirely possible that they could simply reveal publicly and then defend each other for the rest of the game. If there is a reliable investigator, they could also both be checked out. Now it is almost impossible for these two roles to die. They won't be lynched or murdered. Add a serial killer/lone wolf role. No matter how awesome this particular role, this role will not be able to defeat the two basically bulletproof roles. And that means that the game has the potential to be broken and unwinnable for the Serial Killer role. He cannot outvote or murder the two defenders. So no matter whatever else happens, the Serial Killer will always lose to this duo in the end.
In theory you could give the Serial Killer extra voting power or the ability to somehow murder through protection, and it could possibly be balanced that way. But at the same time, the game is still fairly unbalanced because until those two roles are dead, everyone else in the game is much more suspect and liable to be voted en masse and slain at the request of the two nigh-unstoppable innocents.
Even if you made it balanced, what happens if the game events unfold in such a way that the balance is disturbed? Suppose one of the two defenders is killed right away.... in your zeal to balance the game, you've made this incredibly powerful Serial Killer who has abilities tailor-made to match your potentially unstoppable innocent duo. But that duo no longer exists.... the game has become very unbalanced because an intended element to stand up to the uber-powerful serial killer no longer exists, and the see-saw is tilted too far in the other direction for the game to be balanced. It could just end up being a one-sided slaughter, all because the game host didn't make proper preparations for the eventuality of an early power role loss.
So far:
1) Make sure the game is winnable by all sides at the start of the game.
2) If one of the balancing elements is removed early on, make sure the game is still winnable for all sides. Otherwise one wrong lynch or murder ends the game and all the suspense is sucked out of it.
Some game hosts loathe to make basic roles, so they start passing out abilities and personal goals to everyone. But after crafting some awesome abilities and personal goals for over half the players, they start running low on ideas and just throw something together at the last minute. So now you have:
LAME ROLES.
Example:
Your objective is to locate character A using your scanning power. Your scanning power is useless for anything else. Your personal goal is to make sure such and such a character doesn't die. You have the ability to protect said character one time. But since you don't know when they will be attacked, your personal goal is nigh-impossible. And it is far more likely they will die before you even find them. If you do find them, when do you protect them?
I understand personal goals where you want so-and-so to survive, or wish to outlive so-and-so. That's fine as a stand-alone, throwaway, bonus points kind of goal, but when that is all that person is focused on, and they barely have the skills to accomplish that at all, then the role is pretty weak.
It is just taking a basic standard innocent role and giving it what amounts to a bogus, unwinnable mission. As if that player's character is given busywork.... sure, lynch some scumbags, but also do my taxes. It's not very interesting, and the whole concept is forgettable.
Given the near impossibility of accomplishing that goal, it's not even worth focusing on. Meanwhile, someone else might have the inclination to kill a certain person, and have the ability to murder them outright. It's a far easier goal to accomplish. Which of the two personal goals do you think will be fulfilled by the game's end?
3) Every player in your game is important. Make sure they have realistic goals and a realistic shot at accomplishing said goals, even if it is difficult. If you give them an ultra-weak role and a lame goal and nearly no chance of accomplishing it, that person's enjoyment of the game could be affected. Meanwhile, Johnny with the powerful role and the easy goal accomplishes his task, simply because he was lucky enough to be granted the easy role.