I think the absence of major male characters in FiM (the other series we're seriously lacking male characters) only seems large because it's so different from the norm where there's barely any female characters on a show. I might be in the minority, but I think there are plenty of important male characters in FiM and would hate to see a stronger male influence because I can get that pretty much anywhere else.
We have as recurring named male characters who do important plot related stuff:
Spike
Big Mac
Shining Armor
Discord
And male characters (that aren't the ones named above) playing important roles in many episodes, IE: Boast Busters, Dog and Pony Show, Over a Barrel, Sweet and Elite, Baby Cakes, Super Speedy Cider Squeezy, A Friend in Deed, Putting Your Hoof Down, Dragon Quest, Ponyville Confidential, MMMystery on the Friendship Express, etc
That's more than can be said for gender equality in most cartoons.
We're not talking about male
characters here anyway, just male
ponies, so Spike, Discord and any non-pony characters have no relevance to the matter at hand anyway.
Of the ones left, I still think it's a shame the only regular male pony character (Big Mac) barely talks, and the other (Shining Armor) is merely a guest star, i.e., relegated to a select few episodes. Not to mention there's this air of awkwardness whenever they enter the picture (which is very annoying imo). It's slowly getting better, but for a while just having a male pony say a line seemed like an event in itself. In that regard, characters like Mr. Cake and the Flim Flam Brothers are much better written, but guess what: they're not regulars.
I don't see a reason for this happening, especially since, unlike Transformers, with which Hasbro keeps consistency with the characters and such, with My Little Pony their main goal seems to be tear down the history of the franchise and begin anew (with a few bits taken from G3), so why not bet on the guy side of things as well? There's plenty of guys who like ponies, and I'm not even talking about bronies at this point.
You mention you'd hate it if FIM had a stronger male presence because you get that in other shows. Well, I hate it that
any franchise has to, or come close to be gender-locked, and that goes both ways. I hate it that the Disney Princess line is so heavily female-oriented. I hate it that Transformers and Power Rangers pretty much ignore the female demographic. I hate it that nobody ever thought of making a Magical Girl team with a magical boy or two.
MLP to me is just jarring in this because it refers to an entire race of horses, and in FIM's case, it's made even worse because the existence of male ponies is clear. Let's put things in this perspective:
Care Bears has more gender equality, both in the fiction and toylines.
Care Bears.
As for other cartoons, that's a whole different topic, so I'm not going to discuss it.