Actually, a section on "What is side-decking? Why should I side-deck? What should a side-deck aim to do?" at the front of the article is a good way to introduce the guide, over "Hi guys! Side-decking is important, remember you only have 15 cards, here's the article on what you should consider when building it," which is one of the points Cirrus was making, which (i think) was a separate point from the personal choices used in the article.
Basically, the biggest issue with the article progression that I can see is that it ends up kinda melding "Building a side-deck" and "side-decking" at some point, when they should be separate because they're two separate steps (You build the side-deck, then you actually use the side-deck). Personally, I'd probably go like this:
What should I consider when building a side-deck?
Sub-Point (What are my main deck's weaknesses?)
Sub-Point (What's being played where you plan to play?)
Sub-Point (Building to counter opponent's side-decks)
How should I side-deck while in-game?
What is your opponent playing?
Let's say this is may main deck, here's my local area's meta, these are its strengths and weaknesses, cards to consider when making a side-deck?
(Insert very mediocre deck here, or even an outdated meta-deck)
This isn't necessarily "Build like this, Side like this, Win". It's giving your article logical progression and a clear separation between building a side-deck and actually side-decking.
EDIT: Oh right, something else to note. It may be a good idea to link your cards to their respective pages on say, Yugioh wikia. It's probably best to assume that new players aren't familiar with a lot of the cards or archetypes you're talking about, so a brief descriptions on the archetypes might be a good idea too.