I suppose you could make everyone else qualify earlier than the champions....
That would definitely make sense, but it'll also never happen. The whole point of the group stage was to give the big teams guaranteed six games, plus at least another two unless they finish bottom of the group (with the third place dropping into EL). Now they're expanding it to ten group games. But none of that would be guaranteed if they had to qualify in the first place. Originally, most teams had to qualify, big leagues had fewer places, but big clubs applied more and more pressure and got more and more concessions. I can't see them giving that up any time soon.
The opposition to ESL was led by this "earn it" slogan, but these days some earn it by finishing fourth domestically while most domestic champions can only dream of one day participating. And, to be fair, most of those top four teams from big leagues probably are better teams than most domestic champions, but they should still earn their place by playing qualifiers against those champions and showing they're better on the pitch rather than take their place by default. But like I said, it'll never happen, there's no way back.