If it is a stick shift and you raise the motormount or drop the skid plate it changes the geometry of the stick. Some people don't like it. And in my case it caused me not to be able to get it into second gear easily. I ended up doing an SYE so I could get my shifting geometry back. Of course you could possibly heat up and bend the stick but I like mine in the stock position.
I just put a two inch lift on the girlfriends jeep from a 3 inch lift and she had a 1" skid plate drop. I hated her jeep but when I swapped out her springs I took the drop completely out and it drives fine. BTW Mine is a 98 and hers is a 2000 both 4.0 ax15 5speeds.
Now that I put the stick back where it belongs she likes driving it much better. I do too. Her drive line is still at a good angle I could probably go another 1/2 inch with no issues. But I would say that is about it. If she wanted to go any more I would SYE it especially if you can afford it. The most expensive part of the job is the driveline. So if you can find a cheaper place locally you might be able to find a better deal, but the total cost I paid for mine was 500 bucks. If I remember correctly it was 300 for the driveline and 200 for the other parts give or take 50.
If it is an automatic I don't think it changes the geometry of the shifter, so you probably wouldn't even notice a transfer case drop or motormount lift.
My .02