This was also a big concern for me. :C
I just assumed that perhaps eventually, once we got to a certain point in the story, we'd be able to customize them. However, it seems quite clear what they're going for. Not only are we not able to customize companion armor, but if you replace their weapon ingame, it doesn't represent in the cutscenes. They still display the weapons they're intended to have. This is rather telling of what was intended.
I completely understand the creative decision to keep the characters within their defined, prescribed parameters, but it is still quite saddening. However, if you look back on all the previous content in the game, you'll notice that you're not able to customize anyone but your followers... And when you realize that Lana, Theron, Senya and Koth are all the main characters of the storyline you begin to understand why they didn't want you customizing them. At least not yet.
That being said, it's disheartening to see something like this happen when we've already been able to equip our companions in the past. The issue is when you begin removing features; taking away things largely adored by the majority. If companions were not customizable from the start, this decision would've made more sense and would've been consistent with the rest of the game.
I do hope that at some point, we'll be able to equip them, even if it's after all the story content (which is fantastic thus far, btw. Well done BioWare. Let's just hope EA doesn't start charging us for each episode in the future).
Edit: One thing for the devs to also note is that there is an unfortunate side effect of this particular decision. In the pursuit of trying to make the game more immersive, you may have made it less so. Not being able to interact with our companions in the manner we have before can lead us to become detached. It certainly has with me, and after witnessing the death of a certain companion, I'm afraid to get more attached to any of the others as I'm afraid they might be taken away from us in the next chapter. If this was indeed the case, to avoid getting attached to our companions lest they die... What was the point? And what was the point of even implementing a companion inventory reclamation system? Sure, to retrieve any weapon we may have equipped them with, but this could easily be used to retrieve their armor as well (were we able to equip them with such).