Serious series (such as Ultraman Nexus or Kamen Rider Kuuga) can be done very well at times, but a prevailing notion is that darker=better. I've seen this recently with Kamen Rider Gaim, which had a great plot (if suspiciously similar to PMMM) with beautiful designs but a lack of characterization and decent female characters. There is also nothing wrong with lighthearted series such as Den-o or Max or series which are in between like Ultraman Tiga.
So here I'm going to put in a few problems "darker" series often run into which should be avoided if possible.
- fridging: "Fridging" is a term used to refer to killing off female members of the cast to create drama. It is usually looked upon as cheap and weak writing. It's fine to kill off any character as long as it's done right, but simply killing the main character's girlfriend so that he has a motive is lazy. For instance, the death of Goh's girlfriend in the Return of Ultraman.
- Male and female characters should be treated equally: no killing of women for shock value only. SolZen's Ultraman Orion is a good example of a serious series which treats female characters amazingly well.
- As I said before, character death is fine! You just shouldn't kill of a female character for the sole purpose of moulding a male character.
- Nihilism is the idea that hope is false and no matter what you do you can't change your fated doom. Well, not exactly, but darker series (such as PMMM, which I personally really like) can border on it. No matter how serious things get, there should be hope, there should even be some joy. Christians like to tell about their martyrs giving their lives for God joyfully because they have the truth.
- A hero willing to sacrifice himself (or herself) for everyone else is the very essence of Ultraman! This is full of symbolism and really beautiful and classically ultra.
- Don't sacrifice character for plot. This is my opinion but when a series focuses to much on the plot and less on the characters it's not as enjoyable.
- Don't have characters needlessly suffering. Have a reason for it. Convey some message, show how bad the villains are a la Ultraman Leo, go wild, but don't just have darkness for the sake of darkness.
Finally, remember that any tone you choose for your series is valid, they are all equally valid, and everybody has their preferences with which type of series they enjoy.
What I'm trying to say is that tragedy has to have a meaning. If it is tragic to be simply tragic, then there is no point. If you kill of every living thing in the universe to convey some great truth, it can be beautiful. If you kill off the main character's girlfriend to kill off his girlfriend, it's pointless tragedy.
So have fun, and let your series be as dark or as light as you want, because in the end, it's your work.