Although I'm having trouble finding it, there was a response about this before the new champ select even came out. IIRC the problem was that the system was too counter-intuitive.
The following is my interpretation of this, not the official Riot response.
You have to remember that the League community isn't representative of the average League player. The average League player is someone who plays a normal game once in a while and maybe a ranked game in some rare cases. They probably don't watch many guides, don't read patch notes and don't keep up with the PBE. For this kind of player, the option of fill except for X is odd because normally you select stuff that you want to play.
You might be thinking "we can just write instructions!" The problem is that unfortunately, users don't read instructions, especially if they think they know what they're doing. After queuing up many times in the past, a user won't bother to read instructions whenever they select fill. The amazing thing about the current layout is that it doesn't require any instructions besides "Primary" and "Secondary".
The lack of instructions means that all five players can fit onto one screen, whereas writing any instructions is going to take up a bunch of space that will have to be taken from somewhere else. You can either take that screen space when the player selects fill, making that one option change everything and look odd or you can have that space available all the time, which means having a big empty space whenever the player isn't selecting fill. Either way, things don't look as nice and you're still going to get a bunch of people not reading the instructions.
If you disagree with this, that's perfectly fine, honestly I have some doubts as well. I just want to let people in this thread know that Riot has already responded to this, although again I'm having trouble finding it. I suspect that it might have been on Lyte's Ask.fm, but he deleted his account which shut down his page, making his responses inaccessible.