Equilibrium was an amazing movie, and I wish it had been better received, but I think your assessment was correct. First impressions are no joke, and they made bad choices with how to introduce the protagonist.
The Matrix has its own set of flaws (No! That's not true! That's IMPOSSIBLE!), but nobody can deny that the first film follows a very effective formula.
Haha yeah, the matrix did it amazingly (one the first movie) everything was thought out, like before we learn Trinity can fight, they build tension..
"She's just a tiny woman".. "Your men are dead!".
And then she levitates and blows the audience away.
In Equilibrium, you could see that the director couldn't give too shits about the build-up nor the audience for that matter, he just wanted to get quick to what he loves, fight scenes in techno-music.
The story they had to work with was amazing, however.