I'm using a Tau Commander as my reoccurring villain in my game, well, that and Hive Fleet Betrayer, but for the purposes of this post lets just focus on the Tau Commander.
First off, as a commander they don't have to have direct exposure to the commander for him to be against them. His colors can be present, his orders, his troops, etc, etc. Granted, at some point they will have to meet (at which point having Touched by the Fates is a great trait to have just in case), but there are other ways to work it. For one, when this commander meets the kill team, it will be on his terms, and on ground he has prepared. For another, he will know when to cut his losses and run should the KT do amazingly well. The last part, and this is true for all the fights I run, he will be able to win.
I am also going to be building him up in other ways too. Letting the players have small victories, while the commander wins the overall battle. So, yes the mission was successful, the players won, but at the same time the bad guy also got what he wanted. In this way, hopefully I can convey that he is a serious threat, and needs to be taken seriously.
The big thing with villains is to make them smart, and play them smart. The rest should carry over well. Also, when you can, hit the players where it hurts, and hit them hard.