he likes vampires, at least the non maniacal ones (Sybille Stentor for example), which is why he doesnt like the Dawnguard and their "kill them all"
mentality, on the other hand Harkon is a psychopath...
ah well, guess im going vampire
For RP purposes, based on what was written here, thee is little known at this time about either side. Thus, choose the approach that best suits that character. Over time, one may see Isran mellow due to the interactions with Serana, or witness Harkon go further down the rabbit hole, but time is required in character to view this.
I often stay mortal for as long as possible, and then when forced to make a decision, choose the apparent lesser evil.
As far as story and side quests, I prefer the Dawnguard material.