1. You're correct in that he's short, and yes, he's a bit overweight and unathletic now, but at the time, he was far more athletic than Ennis currently is. Felton was one of the quickest PGs at the combine the year he went to the draft, and he ran the fastest sprint time as well. And in the vertical reach measurement, he was middle of the pack, and ahead of Chris Paul.
2. By the time Felton entered the draft, he had become a 44% 3 point shooter and he was far better than Ennis currently is in terms of finishing inside.
3. I think Ennis is like Trey Burke in the fact that he's as good as you'll see in terms of being able to handle the ball, but he doesn't have a killer cross over or anything like you see with elite PG prospects. Felton was no Chris Paul or Deron Williams (the two PGs that went ahead of him in the draft) in terms of having a killer crossover, but he was still very quick with his handle and could beat his man off the dribble with ease.
It isn't about what elite qualities Felton has now. It's about what he had back in 2005 that scouts believed would translate to the pros. At the time, he looked to have all the makings of a great PG.
At this very moment, Ennis doesn't have the quickness, speed, leaping ability, cross over, finishing ability, or defensive ability to give scouts the impression that he should be a lottery pick (IMO). I'm not saying he never will, nor am I saying he won't have a nice, long, NBA career. But I can't imagine a scout watching him play and thinking that he's worth using a lottery pick on at this point.
Edit: If you want to take a look, I just found Raymond Felton's scouting report from when he was in the draft:
http://www.draftexpcomress.com/profile/Raymond-Felton-5/
A couple quotes from it:
"With or without the ball, he is one of the fastest guards in the country, college or pro. His explosive quickness allows him to beat defenders off the dribble and dash past defenders in the open court. He can change speeds in an instant and is rarely caught off balance. On the break, he has the ability to rise above the rim and finish strong due to his great vertical."
"Felton is a rare breed these days. He is a true pass first point guard looking to get his teammates involved before looking for his own offense. He has incredible court vision and sees things develop long before they are there. On the break he is deadly. He can make difficult passes look easy and is not scared to make those passes, even in traffic."
"On defense, Felton is a tireless worker, showing great energy, desire and anticipation. He has incredibly quick hands which allow him to get to many errant passes or loose balls. He also has exceptionally quick feet and he knows how to get position, which makes him tough to beat off the dribble."