Unless you edit the .txt, the orders themselves will feel odd, as many of them use different letters, plus there are quite a few different commands.
You will have to get used to the fact that you cannot click destinations exactly where you want a lot of the time, because of the nature of the maps now. If you played CMx1 in height 3 or 4 typically, you will be in height 2 or 3 now.
You will miss the ease of determining LOS, but love the extra targetting options.
Calling arty is wildly different and a big improvement.
Some troops in a squad having LOS and some not takes getting used to.
There are millions of others, but thats a few things you will notice quickly.
Of course, the biggest difference is the absence of Mr. Borg, for which we give thanks.