Keep Wataru's allergies around longer.
Boost up Shizuka's role. Make her more important to Wataru and the plot in general. And have her understand that this whole Fangire business is going on.
Have more actually horror stuff in it.
Emperor Form needs some weaknesses. Therefor, the other forms can shine more. Oh, and have Wataru become a dragon more often!
Have the people in 1986 actually kill some Fangires! :redface2:
Instead of both 1986 and 2008 repeating the same stories over, the 1986 portion should give some hints to what's coming in 2008.
If Nago and Megumi are meant to get married in the end, have some romance stuff actually going on with them earlier in the series.
Have Shima more involved in the story. Don't make him "important" just in the end.
Have Kengo be like a big brother type character to Wataru. And leave it as just that. Have Kengo help Wataru grow as a person.
Give the Three Arms Monsters more story. Not just Jiro. Oh, and get rid of Jiro's coffee obsession. :redface2:
Cut out the Maya romance. Just leave it as Otoya and Yuri.
Have Otoya be less of a jerk.
Cut out Rook.
Explain what the Fangires are, and explain what life is like to them.
Introduce Taiga earlier.
Don't kill Mio off.