The actual people who were making the clone engine are not going to answer you. Someone correct me if I am wrong, but here is what I can gather:
Dantarion, the person who spearheaded the project, has decided to all but leave Smash hacking. The team that was making it are ALSO the team that were/are making Project M. That project takes up most of their time, and they view the Clone engine as a cherry on the sundae, if you will, so it's not at the top of their priorities.
Now, doing some investigative work, I've found this pastebin file.
http://pastebin.com/pjcMFj1T
What exactly is there not to get? Pichu as a character has little substance. In Generation 2 he was added as a baby form of Pikachu and that's pretty much what he is: Pikachu Jr. In order to make him unique, tons of animation and coding would need to go into the character when we're already spread thin in those regards with the addition of Knuckles, Roy, Mewtwo, Isaac (?) and Lyn (?), on top of the 10 already confirmed characters we haven't completed yet (Ivy, Squirt, ZSS, Samus, ICs, Olimar, MK, Kirby, Yoshi, Diddy).
In the end no matter what you do he's still Pichu. A character that no one likes, and it's not just because he's a bad character in Melee either. It's because the character was designed as a worse Pikachu, with his only saving grace being that he's cuter in some aspects. Do you want to know why the Pichu Bros. don't show up in movies anymore? Because no one likes Pichu. He's a joke of a character and it'd be an even bigger joke if we included him in Project M. I'd rather have no 6th clone than the option of adding Pichu with no drawbacks.
It was posted on July 25th, 2012 to PasteBin. I cannot confirm this is definitely the Project M Backroom, but I can confirm that they post things on PasteBin all the time, as well as this is in their style. It also, looking at the time of posting, maybe minus some time, would fit with the "10 already confirmed characters we haven't completed yet."
Assuming this is them, we can confirm that they plan on adding Knuckles, Roy, Mewtwo. Now, they've said before they will not add ANYONE to the roster if they have to remove someone else, which means that they have the Clone engine, and that it's working in some state.
This lines up with a thread that Dantarion posted a little while ago.
http://smashboards.com/threads/clone-engine-ae-2012.325184/ In it, user Jaklub said
I don't see anything happening what is this
to which ds22, a known ProjectM developer replied
If you only knew what I know...
Keep in mind, this was posted almost a year ago. The Clone Engine has probably been updated to a usable state since then.
There is a lot more evidence leading to my conclusion, but here is my summary:
TL;DR Project M developers have the Clone engine working to some beyond-alpha extent, and are refusing to talk about it.
I am not trying to be accusatory. I am just laying down the facts.
