It fully depends on what you are doing and a little on which pet you use , if you are doing instances then the right resistance when boosted will help your pet to survive , I know several hunters that respec their pets depending on where they are going as it is a cheap thing to do unlike hunters talents.
On my main at 70 i rarely use all the training points anyway , so when i do go in an instance i can easily boost my pet depending on where i go and what my pet gets attacked by.
I am guessing there are as many different ideas on pet training as there are for the best talents for the hunter , so i hope others will give their views on this..