A bad feeling about first published papers I was taking a look at my first published papers, which are published in (peer-reviewed) A*/A/B level proceedings. Thanks to these papers, I finished my PhD a few years ago. 

I was surprised by the quality of the papers and I felt ashamed that I wrote these papers -Of course, this was not my feeling a few years ago-. I found that my assumptions were naive and the conclusions can be valid only for the used dataset (there is a high chance that they are not valid for other datasets). I found also that I lacked some fundamental knowledge and I could explain my approach differently. 

Overall, if I receive these papers now as a reviewer, I would definitely recommend to reject them. 

I don't know whether this feeling is just because 1) I gained knowledge over the past years, 2) the domain (CS) has evolved significantly or 3) the papers were indeed bad and they shouldn't be published. 

In the case of (3), I am wondering what I should do.
You should do nothing other than continue growing and learning. The most common reason would be #1. I can't say the most likely reason is #1, not having seen the papers. 

But a lot of authors, even poets, look back on their early work with a sense of wonder about how they could have been so naive. It is a sign of growth. 

Yes, #2 is probably also a factor to some extent as CS has been a fast moving field overall, not being much over 60 years old, compared to, say math and such. 

And you haven't said that the papers are actually wrong, just a bit naive. Hopefully we all learn some things as we grow older. It normally happens because we are actively thinking about things. 

Others at the time (reviewers, editors, advisors) thought that the papers were fine for the time. They were fine.