The plot-moving elements of "Kiss Me" (IE- Anthony sneaking into the house, and conspiring with Johanna) are still there. They occur off-screen and are explained later through dialogue. The plot elements of "Wait" could've been boiled down into dialogue, sure. But they chose to include the parts of the original score that would translate best onto the screen. And you know what, 'Wait' worked extremely well on-screen. I wasn't bored. Burton made that song, set in one very plain room, visually interesting.
Quartets such as Kiss Me do not work well on film. It involves two completely different groups of people in two completely different locations. All singing different lyrics. On stage, you can buy that S.R. is a London street, and that S.L. is Johanna's room. On screen, you'd have to cut back and forth and have Party B's off-screen voices singing while Party A is on-screen. And it wouldn't be pretty.
Not to mention, it would require the inclusion of Ah, Miss. And the full version of Ladies in Their Sensitivities. Which, totally, would add approximately 10 minutes to the run time of the film.
The Johanna trio worked well because it has one primary singing character, with Anthony and the Beggar Woman having "solo" moments. Compared to Kiss Me, there is very little overlapping.
The thing is, even with all the cuts to the Anthony/Johanna plotline.... it didn't lose much. They were really just as developed as in the show (not a whole lot). The same events still happened, even if they weren't shown.
"...everyone finally shut up, and the audience could enjoy the beginning of the Anatevka Pogram in peace."