Someone please correct me if I am wrong, I am currently in the process of trying to craft a wand myself, and it has been a nightmare to say the least. Since you Fractured +6, I assume you do not care about Sanctification to try and hit +7.
I assume that Spell Damage would be the most universal and best scaling stat to get as a third prefix, Considering it's T2 Cold damage, the minimum Ilvl for it is 70, same as T2 Cast Speed, so Whittle would remove either one of those. Keep in mind that T1 Spell Damage is ilvl 80, which means that if you get T1 Fire/Cold/Lightning/Chaos/Physical, they are all ilvl 81, which will then essentially brick your chances of getting T1 Spell Damage, without gambling a 1/3 with Omen of Sinestral Annulment to try and remove it.
Essentially, in order to reroll Increased Mana Regeneration Rate (T1, ilvl 79), you could either gamble the 50/50 with Omen of Dextral Annulment, if you really want to try and keep that T2 Cast Speed.
Otherwise, you could Omen of Light the Cast Speed, then Essence of the Abyss with Omen of Dextral Crystallisation, which will only add a desecrated Suffix, since your prefixes are filled, removing T1 Increased Mana Regeneration Rate.
I believe people prefer to fracture T1 Spell Damage for the following reasons:
It prevents you from getting T1 Fire/Cold/Lightning/Chaos/Physical on your Prefixes, meaning you can either block mana with desecration, Perfect Exalt slam for 1 x T1 Gain Elemental Dmg%, omen of light the mana, and use desecration to get another T1 Gain Elemental Dmg%, or if you want to save desecration for suffixes and feeling lucky, slam Perfect Exalt with Omen of Sinestral Exaltation in hope of hitting T1 Gain Elemental Dmg%.
Before dealing with prefixes, you would probably want to Chaos Orb spam for +6 to level of all Spell Skills. Then, after you are done with prefixes, you would add a suffix, hope it is not T1 Increased Mana Regeneration Rate, because Whittle would then remove +6 to level of all Spell Skills, and try to Whittle for T1 Cast Speed, then T1 Critical Hit if that is what you are after.
Getting T1 Increased Mana Regeneration at any point, would endanger your +6 to level of all Spell Skills, because +6 is ilvl 78, and Mana is 79, so Whittle would remove the +6.
Basically, it seems that when crafting Wands/Staffs, the decision you make is between suffering through Prefix/Suffix hell, since both T1 + to level of all Spell Skills and Spell Damage are prone to being Whittled, if you hit T1 Fire/Cold/Lightning/Chaos/Physical on prefixes, or T1 Increased Mana Regeneration Rate.
Personally, on my Wand crafting project, I fractured T1 Spell Damage, yolo slammed two Perfect Exalts and got T1 Gain as Cold and Lightning. Now I am trying to add T1 Cast Speed, in order to Whittle for T1 Critical or +4 to all Spell Skills. The problem is, if I hit + 5 to any element, I will have to essentially gamble removing cast speed or +5 since +5 is higher than T1 Cast speed.
All in all, it feels like a crafting nightmare, unless you settle on +5 to a certain element, after which you can essentially whittle for T1 Cast speed, and then T1 Crit or Crit damage, because Whittle will never hit +5 or Cast Speed.