In the smaller version, samples seem to be chopped off at the beginning, which is very annoying. In many lines, there is an audible click at the beginning (like in "Ich brauch aber kein Tutorial"), and in some samples, the first letter is almost inaudible (like in "Du hast hier aber nichts zu sagen"). This was not the case in the older version. Hence, I suspect that something was broken when the samples were reencoded. I have no such issue with Deponia 4, so it's probably not the engine.
I only played it in German. Other languages not checked.

With Deponia 1, setup_deponia_2.2.0.8.exe is fine, and when applying patch_deponia 2.2.1.9.exe, the issue is there, and it is still there when I install the current setup_deponia_2.3.0.10.exe.

I'm definitely not the only one with this issue, as you can easily verify on Youtube.
A recent version where you can hear the issue as described: https://www.youtube.com/watch?v=_crN7_aCz6k#t=1m40s
And an older version with flawless audio intact:
https://www.youtube.com/watch?v=ist68z2zddc#t=2m02s

Please fix this issue.

Sorry, but as you can see, obviously we are the only humans left on this planet being able to sense such problems. The zombie apocalypse is imminent!

Rufus is not talking naturally anymore. I suppose some braindead genius had the brilliant idea to remove the silent parts of the voice clips at the beginning and the end to save space.

It becomes ridiculous when Rufus says "Goal? ........... Goal!" in Docs lab trying to wake up Goal, but after the update he says "Goal?Goal!" so fast and unnaturally than I cant even repeat it IRL. The German voice actor did really a great job and now they raped his work.

But since no one cares, it won't be fixed. Maybe he adapted to the world as of today. Peopletalkingno thinkingsonogapsandmuchblabla.

Aber ja, am meisten nervt, wenn Satzanfänge wie "Du hast" immer mit "<click>u hast" gesprochen werden.... Das macht mich noch WAHNSINNIG. Eintauchen kann ich da nicht mehr. Werde alle paar Minuten rausgerissen. Schade.

I have to correct myself: It is the engine after all. When you extract the sound files and load them in your favorite player, the samples are completely intact.
I also got a reply from Deadalic, which explains that they avoided the issue in Deponia 4 by simply not cutting the samples that close anymore.
Sounds more like a workaround than a solution to me. And it certainly doesn't fix the first 3 games in the series.
The only hope is that the engine gets fixed and updated.

I would just play the older versions, which I still have, but unfortunately, they have the bug that some lines get skipped completely, which seems to occur rather randomly. So not really recommended either.
I also liked the backgrounds without compression artifacts in the first two games and didn't really mind that they were almost 3 times the size. With just a few GB, the games are still small in comparison to some other recent titles.

There is an update on this, and another letdown on GOG besides not releasing the Complete Journey here.
Apparently they did upgrade the first Deponia game to Visionaire 4 some time ago, but only on Steam, not here on GOG. That one fixed the audio issue, though.
So far for the half good news, at least good for those having the game on Steam.
The other huge letdown is, that they only did this upgrade for the first game. They didn't even fix the Complete Journey either. And as it seems, Daedalic is now degraded to a mere distributor company, thus I assume, there is no coder left to fix the other games. A very sad situation.

Are there any unofficial ways to upgrade the engine without access to the source code? I'd love to give that a try.