In terms of doubts, are there not always doubts? Or is it that some doubts are greater than others? How often does a ms come in that is so clean and sparkly and perfect that there are no doubts? What percentage of mss do you fall in love with completely from the word go? And have no doubts over?
There's a difference between doubts and things that need work. Editors, being who we are, don't think of any manuscript as being so clean and sparkly and perfect that it can't be improved upon at least a little. So to an editor's mind, there's no such thing as a manuscript that needs no work.
Doubts are when there are things that need work that we are unsure we and/or the author can actually fix. And usually having doubts about a manuscript leads directly (and pretty darn quickly) to its being rejected.
But every once in a while doubts are amorphous enough to cast a book (perhaps like the one we've been discussing) into a kind of limbo--you love it, but maybe you're just not sure about how the market is going to respond. but you love it. but will it work? but you love it. but would it be taking a place on your list that would otherwise go to a more solid bet? but... etc.
Still, and as we've covered, there's just no excuse for three years. Jeez, there are a couple things on my desk that I've had for less than three months and I'm already feeling guilty about them.
Though I do want to add something. While I'm not about to start making excuses for people who take obscene amounts of time deciding about manuscripts, I can't help feeling a little sympathy for them, especially at the end of certain days. It can be a killer job. Sometimes there's less than half the time you need to get all of your work done, and the only thing that saves you from utter panic is the exhaustion. And you wonder why so many junior staff leave for grad school--or sanitariums.