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I've looked at multiple sources with regards to this, but I am still a little confused. Is it really up to my own discretion to choose gems?
Is there a more optimal option for gem choices for someone who just hit 90 and is starting to build a gear set?
What are you confused about ? Gem for your stats. If Protection, get Hit/Expertise on gems until you're able to cap both, then go for either Haste or Mastery on your gems depending on which gearing strategy you adopt.
Go for socket bonuses when they matter, ignore them when they don't.
Yes, choosing gems is at your own discretion, based on your needs.
You're using the wrong gems in your ghost iron dragonling. The 208 stat gems are from cataclysm, there are mop versions that give +600 stats. You can buy them on the ah fairly cheaply. Any three of the following would be good: hit, expertise, haste, mastery.
Hit is more valuable than expertise. If you had to chose one over the other take hit. Some paladin abilities like judgement and avengers shield can only miss, as such you'll get more bang for your buck by getting hit maxed out first.
Since you're just 90 you'll spend the majority of your available stat points getting your hit and expertise up. Don't worry too much about gemming for haste or mastery at this point because it really won't be an option til you get to a higher item level.
As for stats to gem for stamina is generally the worst option because it can make you more inflexible. What I mean is when you don't need that extra health you cannot easily get rid of it for something valuable (more haste/mastery). Stamina is better on a trinket which can be swapped easily for specific fights. For the same reason it is better to not have hit/expertise on trinkets, because you can end up stuck with them to get to your caps and become incapable of swapping trinkets depending on the fight.
There are a few different ways to go, but you'll want to cap your expertise and hit rating before doing anything else. This makes for reliable holy power generation and has the added benefit of more damage. At low levels of gear 320 hit in blue, 320 expertise in red, and hit/haste or exp/haste in yellows works well. You can easily make use of all gem options so it's probably best to match the bonuses.
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