Being able to calculate strike temp and volume without the specialty grains in the mash would be a nice touch.
I just completed my first brew day using Beersmith 2.1. I love the tools it offers to make adjustments along the way and I really like the new timers and cloud features.
After listening to a podcast on the Beersmith forums with Gordon Smith I decided that there really is no need to mash specialty grains (duh). So I had my brewshop bag them separately with the intent of adding them to the mash at mash out.
After mashing in using the suggested volumes and temp, I quickly realized that temp and volumes were off. "Ah, the software is assuming all the grains are being mashed." I thought. I added in the specialty grains and things returned to normal until my digital thermometer went on the fritz (rough brew day).
I don't think it would be too difficult to add a checkbox or something next to the grain ingredients that indicates whether or not they are going in the mash. Even better would be a drop down for each grain like you have with the hop additions that indicate when you plan on adding ingredients and adjust strike temps and volumes accordingly.
The same can be true for adding extract to a partial mash recipe. Some people prefer to add the extract later in the boil but the pre-boil gravity assumes the extract is added at the beginning.
Any modestly experienced brewer can easily work around these things but I know you want to have a product that is as intuitive as it can be.
Thanks for all you do.