What problems did you face when you first began writing fanfiction?
I had it all. Bad grammar, Mary Sues, no description, no good characterization of canon characters, no plots, zero organization, bad handwriting, no discipline, legendaries popping up for no reason. Yes, if you say something bad about fanfiction, most likely I had it in my old fics. I still have them lying around somewhere, so if I can get my scanner working, you may see how horrible I really was.
What 4th-gen Pokemon do you see to be used more than others in fics?
I don't read a lot of fanfiction anymore, so I can't say. I do remember, however, that there was an abundance of Lucario running around. Do not get me wrong. I love Lucario. It's just that there are many other Pokemon out there that can be used. Unless the Pokemon is needed to fulfill a particular role, like Gummy's fic. (Did you enjoy your shameless promotion, friend?)
I don't remember seeing any fics with the Shinx line. O_o
Aside from TurtleKing's fic, there is a fic that should be somewhat familiar with SPPfers that I can recall that has a Shinx on the main character's team. Other than that, I don't really remember any other fic (aside from my planned Sinnoh one.)
Just as a piece of somewhat good news, my fanfic is now in version 6.2 (yes, 6.2 copies of it flew around at some point in my room), and being rewritten over to a "clean" unedited copy.