As of right now, you're stuck with gameplans... no way to delete them, so the best bet it to copy from your main ones and use them as 2nd half adjustment gameplans.
User 1 and User 2 are great features and I beg to differ that they are not very important. I have very specific guys that I want to play in very specific positions on the O line, particularly at center. If I plug in 3 guys at the "guard/center" drop down, the cpu will randomize who they are, but I want a very specific player at center, so I use the "User 1" option for center. Same with nickle and dime or the 4'th LB in a 4-4. I can put exactly who I want in those positions, and I can tell you after toying around with different players against different formations, it does make a difference who you have plugged in at certain positions. I can easily assign who/where I want the extra DB(s) in dime and nickle.
No deletion of gameplans is kind of a drag, but I've found ways to use the old ones easily with all the new copy/paste features, but the User 1, et.al., options are one of the better points of Beta in my opinion.