I've been to both Alinea and L20, and I don't think you can go wrong with either, as both are amazing. However, I think that Alinea is a bit more playful, a bit more entertaining. And, of course, you have to like seafood pretty well at L20 -- though I will say that the pork belly is unbelievable, so it's not all fish.
I think part of the reason I lean toward Alinea is simply because I've been a fan of Chef Achatz since his days at Trio, where I indulged in lots of his inventiveness before it got to the level of sophistication it has now achieved. So I feel connected.
But you really can't lose with either. Both have great food and splendid service.
I think Alinea is a bit more theatrical -- in a good way. It's a whole evening's entertainment. L20 seemed a bit more intimate, and a bit more elegant.
There is no bad choice, however.
Tru is good, too, but a bit less special. However, Tru does have the coolest ladies room of the three.