Why is everyone okay with this? The CSR ranking system has serious issues.

Agreed.

Players end up getting a different rank every season because of their luck with teammates.

Placement for a new season after you've already been placed doesn't effect your rank greatly. I don't have enough data to support this claim but I don't think it effects it at all.

The rank they get after qualifying never truly reflects their skill

Your rank after qualifying is never going to reflect your skill level. It's to put you in a good general place so the MMR system can stabilize a bit.

The fact that you can go 25 and 3 but lose due to crappy teammates and get punished because of it is absolute bullshit.

If you can't carry Onyx trash you ain't a shitbird, playa.

I was initially platinum in swat and almost reached diamond. The other two times I qualified I was silver and bronze.

I imagine this was the release system, then the following seasons were with the tuned system that places people lower. It it VERY difficult to get Onyx. (Then after you get Onyx the real challenge is finding match.)

It's all over the damn place. Why does everyone seem to be okay with this. Basing your skill level off strictly wins and losses does not accurately reflect your skill level.

You're wrong. On the internet. The worst type of wrong.

Your skill level should be based off your individual performance in each match.

Then everyone would bait everyone all of the time.

I don't know why everyone has praised the halo 5 ranking system as so great when it has this fatal flaw.

I don't think anyone has really, it is certainly fundamentally flawed. But for none of the reasons you think it is.