I know exactly what you mean. I also think about the same things, but I’ve managed to cut down somewhat. For example, I always felt robotic when putting on the tallit/tefillin in the morning. I solved that by getting to shule about 12 minutes early each morning; I’m not rushing to get them on, and I am able to take my time and put them on in a meaningful way.
In general, for me, as long as I’m not rushing to get things done, it makes it easier to feel like I can put some meaning into what I’m doing.