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I'm not joking, nothing you suggest is actually optimal.
Runes - a complete mess. There is absolutely no reason to splash your runes so much with unnecessary and sub-optimal stats.
Items - Annie is a burst mage. It might be useful to buy an early Haunting Guise, but upgrading to Liandry's Torment is definitely not the right idea in about 90% of games. As for your other suggestions, in fact, if players can get away with it, they would rather build Annie as a secondary AP carry with a Ruby Sightstone, rather than build weak items such as Locket of the Iron Solari. Frost Queen's Claim isn't that strong either.
Skill Sequence - Absolutely horrible. You don't even have the basic grasp of how to skill a champion. In 99% of cases, you max two abilities at level 9 and 13. However, it seems you also failed at the following part, which is prioritising the skilling of the right ability, which you have not. On Annie, the first ability to be maxed should be W, not Q. It may have lower range, but higher base and scaling damage than Q.
Masteries - The following masteries shouldn't/should really be taken:
Enchanted Armor - Gives nothing early game and by the time you get to late game, the amount of armor you can build through items makes any extra benefits gained from this mastery negligible.
Summoner's Insight - this is time off Flash and Ignite. Why the hell WOULDN'T you take it?
In any case, offensive masteries are actually better to run than focusing on defence/utility. You don't pick Annie to be tanky or even necessarily useful past her one stun per rotation, it's her terrifying damage.
I read some parts of your 'guide', but it was also mostly wrong.
To put it simply, my review of your guide is this:
You should be using guides, not writing them.