I continue to use the regular lineup tool in HT because that is what I have become familar with. But long ago, I started figuring out my lineups on paper, where I arrange the players in a 4-4-2, and then use arrows to indicate repositioning and individual orders. So if I am using a 3-5-2, I'll place the 3rd IM in the back line and then draw an arrow up between the other two IM. If one of the IM is a played defensive, I place a small arrow next to him. This is enough for me to visualize the actual positioning, but allowing simple data entry, as I walk through the 1-4-4-2, using the pulldowns to select the player and his re-positioning/individual orders
I think the layout of the BB lineups are confusing, the starter positions are layed out left to right (1-5), with the vertical position used to indicate players toward the center of the court or more to the wings. But the substitute positions are laid out vertically (1-5).
I don't really think of the lineup as 3 separate teams, but rather a 5 separate depth lists, one per position. So that is the way I work things out on paper, and even if I have a player listed in two posiitions (starter at PG, 3rd at SG) this is easy to see.
If this were a hockey sim, it could make sense to define the lines and defense pairings as a team, but BB treats players more as individuals.
And because of the depth charts, I think that drag and drop would help a lot, because that is simply an easier way to re-order a list.
Simply changing the arrangement of the pull down menus would help me a lot for the current system.