I actually feel about Alex the way you feel about Sara. I don't think she could have ever trusted Neal completely and vice-versa. When they saw each other, one of them always had an angle and/or wanted something from the other. They never met just to be with each other. The show is currently keeping me company while I make decorations for a cake and like Mozzie said, Neal and Alex were convenient.
As far as Sara is concerned, I think, the time would have come when she would have had to choose between her head and her heart. She seemed to have genuine feelings for him, she just also knew who he was and she needed to deal with. If the relationship had gone on, she probably would have had to decide if she's willing to accept and live with that or not.
I think she was intrigued/attracted by who he was. Could it have worked out? I don't know. But I liked them, so I like to believe it could have.
I bought it. Or, I guess, I'm willing to believe it was real. But we never got to see a lot of their relationship in general, so it's very hard to say. Although, if Kate conning Neal would have been the route they wanted to go, they probably would have hinted at it.
I think they were more alike than they seemed to be at first glance. Sara didn't mind coloring outside the lines, she said herself that she often operates in grey areas and stretches the law. I don't think she ever would have become a criminal or if she would have been able to accept that the Neal she got was the Neal she got and I don't think Neal would have completely changed either. But the life he had built in New York and/including Sara were the reasons Neal had so many doubts about leaving New York when they had the Nazi treasure.
I think what was most important to Sara was that Neal was honest with her; she wanted him to trust her and let her in.