Discouraged Logan only has Romance options with the player (there's a bit of a... "smutty one" but it doesn't feel like smut tbh. Pretty vanilla even, compared to most of what's in the game), while Encouraged Logan has all the Smutty options. Discouraged Logan has some pretty sweet moments, but fuck it if it didn't feel like chore lol. He is sweet though if you manage to soften up his hard shell of a personality.
Honestly, after going through with Encourage Logan... all I can say I can never go back to the Discouraged one haha.
Still it depends on what the player likes, whether it's romance or smut. I just found the Encouraged one better. Smut all the way. I have Rhot to take care of the romance part anyway.