I added labels for a practical reason actually - they are not just cosmetic. A labelled jar cannot accept essentia that differs from its label and labelled jars get priority in the tube network. A labelled jar will actually draw essentia out of connected unlabelled jars.
As for the tubes:
Yeah, I've mentioned in the past that I probably won't add conduits again, but to be perfectly honest I missed them. More importantly however for blocks like the essentia centrifuge in the video I was struggling to think of a good way of getting the essentia into and out of it.
Golems could work, but golems have proven themselves to be a bit of a resource hog. For a large essentia processing system you will need a lot of golems and it may make server admins cry. The next version has a lot of below the hood improvements to golem AI, but they still use a lot of cpu cycles when compared to tubes.
It should be noted that tubes are actually quite a bit slower than your higher tier alchemy golems when it comes to purely getting your essentia out of alembics and into a jar.
Lastly there is something visceral about having to open or close valves to move the essentia around.
Combining essentia:
Maybe. I'm still debating if I should make that possible.