Should I replace my disk brake calipers?
What you describe in the first part of your question is normal. Longer lever travel may indicate you need to bleed the brakes. Uneven caliper piston movement is caused by contamination of the piston seals with dirt.  Park Tool has a video about cleaning pistons and seals.
However this is bit more worrying:

Sometimes the pistons are cock-eyed, extending from the caliper at an angle. Sometimes I notice air bubbles in the lube oil between the pistons and the caliper.

The pistons should not be able to extend at an angle. That's not 'lube oil' between the pistons and caliper, it's the hydraulic fluid (mineral oil in Shimano's case) and you should not be seeing any of it getting past the seals (or leaking anywhere).
This makes me suspect that the seals are worn out. The Park Tool video I linked above shows how they work.
Seems to me that it should be possible to replace the seals in hydraulic brake calipers, but I've never heard of anyone doing it - someone will maybe add a comment about that.
I would not assume that calipers and levers from different groupsets are compatible. I tried looking this up in Shimano's compatibility information but inter-groupset caliper and lever compatibility is not listed for MTB groupsets.