For a long I left everything at default. Part of it was sort of immersing in the aesthetics in the beginning, the way it was designed, that sort of look and feel. Another things is that not everything looks great in the basic colours available and customisation options are a bit of a money sink compared to practical options like slots (especially if you've not decided to commit to the game).
For my first few primes the design was so much better than the normal versions I was only tweaking the colour schemes slightly, re-shading everything, but keeping the overall balance the same. That I only did once they were maxed anyway.
Weapons I barely ever changed anything, yes a lot of those were throw-aways for MR so there wasn't any point and I didn't have many colours. Mostly I slightly tweak the colours on others where the designs don't look quite right, for example the Kuva-lich weapons are green-grey for some reason when they should really be inverse of the normal kuva style.
I have been doing more customisation recently, but nothing to extreme. I think that I'm probably trying to keep everything to that it still fits with the general aesthetics of the game so there's a lot of gold, sentient colour swaps from the Titanin/Limbo skins, and what would fit thematically with the 'frame.