As much as I like Laurie, I don't think he would have ever been intelligent enough for Jo in the long run. I can only say this now that I am actually married.
It turns out, the puppy-love crushes we experience as children rarely turn out to be someone we would be compatible with for life. I think these crushes do more in the way of teaching us what qualities we want (and some of those playful childhood qualities will never change). As we grow older however, physical appearance, charm, even sense of humor (to me) do not seem to keep two people together as well as common life goals and values, and equal intelligence.
Jo was an independent spirit from the very beginning. Her self-confidence would have always overriden Laurie, and as the man in the relationship, I predict he would have been very intimidated in a relationship with her. This does not equal a healthy marriage recipe. They are perfect childhood friends because at that time, Laurie and Jo are very close to equal. As Jo grows into an ambitious woman, however, she leaves Laurie behind. It isn't that he wouldn't want to support her as a thinker and writer - he simply wouldn't be able. And as a result, Jo wouldn't revere and honor him as a man in the way he would need. She wouldn't be able to.
Amy, on the other hand, is not as intelligent as Jo. She is artistically gifted, but not innately smart. Laurie is perfect for her because she will genuinely adore him their entire lives. She will need him, maybe in part because of his money, but also because as a youngest child, she is simply more needy. Laurie will be the sole providor in their relationship - and Amy will respond with nothing but gratitude - which will affirm Laurie as a man.
I think that Amy was a better choice because ultimately Jo always was a tom boy and never really had the spirit to get married and live a normal womans life.