I was recently in two LBS trying to decide between the ALR5/S5 as well. Both shops strongly recommended the ALR.

Of course each rider has to make his own decision after testing, but the salespeople felt that the "high-end aluminum" was noticeably better than the "low-end carbon." In addition, they said that the difference in ride quality between the Emonda S# and SL# is so big, that they really wouldn't ever recommend the Emonda S# over the ALR.

Edit: That is to say, if you are going to "upgrade" from the ALR, you should skip the S and get an SL.