Before I begin addressing the article, I'd like to point out a few things. The first is to bear in mind that this was written in 2012, and that the show has changed considerably since then. The other is that I do believe the author is vaguely skirting around a legitimate point - namely, that the lack of decent male characters in MLP leaves it largely unable to directly address problems exclusive to boys. Despite all that, I disagree strongly with the way the author approaches the issue.
This quote has a lot of points, so I'll address each one seperately:
Spike cannot be a main character because he is a baby dragon: While Spike is indeed called a "baby" dragon, it's generally understood that dragon biology is very different to pony biology. So despite being a "baby", his behaviour/intellect in practice seems to be very similar to the CMC. Like the CMC, most of his storylines involve some form of self-discovery and he is often shown to have something of a child-like immaturity (e.g his whole plan in Owl's Well that Ends Well).
Spike is too "minor" to be a major character: I disagree for a number of reasons. Firstly, even when the article was written, Spike appears in nearly every episode alongside the Mane 6. I don't see how such a character could be considered "minor". Secondly, Spike plays a key role in a number of stories following season 2 - most notably The Crystal Empire and Power Ponies off the top of my head. In both of these episodes, if Spike had not been there, the Mane 6 would've been basically done for - something which one wouldn't really say about a "minor" character.
On Spike's Development and Misandry: The way the author has worded this point seems to suggest that Spike's "male-ness" is the cause of all the problems in Secret of my Excess. In a nutshell, the problem is that dragons (as opposed to male dragons specifically) age by being greedy - and that greed and the person it makes Spike become is the source of the conflict. Based on what we've been told, this situation would logically play out in the same way if Spike were female.
Infantalising Spike: I disagree that the episode infantilises Spike. While he's transformed back into a child on a literal level, like I said, dragon biology is different to regular biology. While he may have grown up on a purely physical level, I think most people would regard "growing up" to be something far more than just physical changes. To have a go at articulating that expanded definition, I would say that growing up is the attainment of adult responsibilities and freedoms. Indeed, despite some people technically being "adults", we will often deny their adulthood if they are perceived as neglecting said responsibilities. Following this leads me to two points: Firstly, to say that Spike is infantalised would be to suggest that his maturity acquired through adulthood has been taken away. This is impossible because evidently he never possessed it to begin with. Secondly, while Spike certainly isn't an adult by the end of the episode, I would argue the lesson he learns is pushing him in the right direction of adult maturity. Specifically, he learnt from his past mistakes that part of being a responsible member of society is to not be greedy. As for the comment about Spike's growth being treated like a disease, it isn't because he is a male growing up. Rather, Spike is rushed about from doctor to vet because Twilight doesn't understand is happening to him. While one could put this down to Twilight being stupid, it isn't borne out of a desire to stop Spike (as a male) from growing up and gaining maturity.
Feminism and Symbolism: As I said previously, the episode is about Spike's greed, not the Mane 6 stopping Spike from expressing or acting for himself. Generally speaking, just because one sees a message in a piece of media doesn't mean it is there.
I agree with this insofar as that Big Mac is basically nothing other than a running joke and would be better as a more expanded character. However, the overarching tone of the article would seem to imply that this is the fault of Lauren Faust (and by extension, Feminism). However, based on what Faust herself has said, we know that this wasn't her intention. In fact, Faust wanted to do an episode where the Mane 6 take Big Mac's permissiveness for granted ending with them having to acknowledge their mistakes and apologise to him. However, this idea ended up being rejected - but not by Lauren Faust acting as a Feminist.
Source: http://www.equestriadaily.com/2012/01/cancelled-big-mac-episode-idea.html
From the way Shining is portrayed in A Canterlot Wedding, I could actually see an argument that it reinforces negative stereotypes about men. Specifically, one could make the argument that Shining being controlled by Chrysallis reinforces the stereotype that men exist primarily as blind sexual beings. However, that doesn't mean I agree with the claim put forth by the author. Despite being controlled, Shining Armour is not a throwaway character for someone else's backstory. In A Canterlot Wedding, both Cadence and Shining Armour have to combine their luvey-duvey magic to defeat Chrysalis. Though he is sidelined more than I would've liked in this episode, if Shining hadn't been there to throw Cadence, she wouldn't have been able to save Spike. Finally, he has an active role in both Canterlot and the Crystal Empire. In the former he served as Captain of the Guard and was pretty much solely responsible for creating the shields around Canterlot. In the latter, he was shown leading the Athletics. He isn't only there so Cadence can have a backstory - in fact, he's played a vital role in several stories.
I'm sorry, I couldn't resist. In all seriousness though, I think the author misunderstands the Feminist argument for greater gender inclusivity in films and whatnot. While I don't agree with everything that necessarily stems from this train of thought, it essentially goes like this: It's not so much that there aren't any women in films/TV, but rather that said women tend to be portrayed in ways which limit the agency of the characters. If people already possess similar ideas about women's agency, then the perpetuation of said stereotypes in media will only reinforce those ideas. Assuming that it's correct, this situation would harm both men and women, in a nutshell because it would cause one to be prejudiced about what a person of either gender is capable of/should do before they have tried to do it.
I addressed this in my discussion of Spike and Shining Armour.
From what we know of it, I would agree. However, given that MLP is marketed to little girls, I suspect the overabundance of female characters is more the result of overly Conservative marketing rather than any sort of conspiracy. Of course, I'm not saying I think this is a good thing - just that it isn't being done because the creators or the show hate men.
Shining Armour is shown to be both Captain of the Guard and is shown to have responsibilities as a prince of the Crystal Empire. Both are very powerful positions. Another example is Fancy Pants. Through wealth, he has considerable power, yet he is from memory portrayed more sympathetically than his stuck up rich friends. Also, it's worth pointing out that most of the major villains (male or not) have aimed to gain power. While MLP doesn't show men in leadership positions that often, there's a big difference between showing lots of females in power and actively saying that men having power is wrong.
One could argue Prince Blueblood, but apart from that this is true.
What the author says of these two characters is true, however that doesn't mean that the show doesn't have an abundance of nasty female villains, with the ones she mentions next notwithstanding - The Maneiac, Trixie and Gilda to name a few. As for...
I disagree with parts of this analysis. While Nightmare Moon was indeed Luna and given pardon by Celestia, that has nothing to do with what motivated her to become evil (what the author's claim is based on). In fact, Luna was motivated by jealousy, so I don't see how that makes her makes her any better than Discord and Sombra as far as having pure motivations is concerned. As for Queen Chrysalis, I agree with the author's assessment of her character. However, given that the show itself does not show her any sympathy at all or draw attention to this, I don't think this constitutes the show sending a message that male villains are worse than female ones. This view also leaves out other female villains who certainly didn't have pure intentions either - for instance Gilda was motivated by insecurity and Trixie was motivated by boastfulness and a major superiority complex. In a nutshell, most FiM villains don't have sincere motivations regardless of gender - hence why they are villains.
Most of this, I've already commented on at some point, but I'd like to clarify a few things. I apologise for being a little more flippant from this point forwards but I'm getting a little tired now (it's getting late here).
Males are seen as a threat: Nope, as I've already explained, despite having a lack of male characters, there are plenty of males who are seen in a positive light.
They deserve no pardon: I probably would've given the author this back in 2012, but given that a major part of Keep Calm and Flutter On/Twilight's Kingdom was to forgive Discord despite how much he'd messed things up, I don't think it really applies anymore (if it ever really applied at all)
They cannot be heard: I agree that male voices tend to be less often heard in MLP than female ones, but as I said, this is much more likely to be the result of Conservative marketing than any real conspiracy. Again, like I said, it doesn't mean this isn't a problem - just that I think the author is getting at the wrong issue here.
Ruining a Perfect Matriarchal Society: It was never perfect to begin with - if it was perfect, it would be a pretty boring show!
I could write another paragraph addressing this, but I'm honestly too tired and lazy right now. So I'll use this image to sum up my reaction:
For the record, I don't mean any disrespect to the author by doing this - I just feel it's always good to break these discussions up with a little offhand humour. It can make discussing someting controversial a lot less antagonsing and intense.
Well, with that I'm finally done! How I spent my Saturday night writing this, I really have no idea... I suppose I need to get out more really.