The ability to book by fare class is one of the woefully missing aspects on online booking. In the early days of booking on the internet, some airlines offered the ability to book each leg by fare class, but that level of complexity was not utilized by travelers (except highly experienced flyers) and they all dropped it in favor of booking algorithms that satisfied the majority of travelers.
While perhaps the option could be added back in someday, I think the number of folks who have enough knowledge to benefit from it or that would be willing to spend the time to do it, is but a small fraction of the traveling public. Hence not really a good ROI.
Travel agents still have the ability to look at each leg of a trip and see how many seats are available in each fare bucket, and put together the perfect combo.
With each iteration, the booking algorithms get a bit better (most of the time ;-), but they will always be geared to satisfy the majority of travelers and hence never quite perfect for everyone.