I've done all the challenges so far. I'm mastery 26 (started late July 2018), but recently got my wife and brother to play. And they are mastery 5 and 11ish. So I'm looking at this from a few different perspectives.
The biggest thing is that I think Nitain should still be available through the old alert system in addition to wolf creds, or maybe every level should give you a Nitain in addition to the normal reward. My brother at mastery 5 needs Nitain. He doesn't play a lot, so he's about to hit Nightwave rank 1. Needs 3 or 4 for Nitain, and then it doesn't appear until 7 or 8. That's hard if you don't play a lot. Like 3-4 weeks for 15 Nitain, and that's ignoring the rest of the rewards. Meanwhile at Mastery 26, I'm already sitting on over 100 Nitain, and I'll be able to buy tons of other stuff since I'll hit over rank 30 no problem. My wife is doing all right on Nitain while crafting new items, because we've been doing all the challenges together. So, the amount of Nitain is probably balanced if you're doing every challenge, but that's not going to be true for everyone. If you're only generating 20k rep/week, that's going to be 15 Nitain/2 weeks or so, if you don't buy anything else.
I also don't like the overflow effect of Wolf Creds. It's extremely limited until Rank 31, and then you'll be swimming in them. I'd rather see wolf creds at every rank (maybe 10/rank to match the 300 you'd get if you did it all). Obviously, I'm not rank 31 yet, and I'm going by the assumption that you get 50 wolf creds every level after 30. I'll hit rank 45-50 probably by the end. That's an extra 750-1000 Wolf Creds, vs the 300 available if you can only hit rank 24. That's about triple the amount you'd get from the initial.
For challenge specific stuff, I think the biggest issue is that some of the challenges feel outside of how the game operates.
1. Ayatan socketing - I do syndicate missions every day and I have access to Arbitrations so this wasn't a problem for me, but I feel like it forces stalling. If this repeats, then I'll want to hold onto Ayatan sculptures and not socket/trade them for endo in case it comes back. I haven't socketed anything since this challenge and don't plan on doing so until this Nightwave ends.
2. 60 minute anything - This game is broken down into 5 minute segments. Basically every mission is designed to be done in 5 minutes. Capture, exterminate, sabotage, rescue can all be done in under 5 minutes. The time locked ones like survival, defense, interception, defection, and mobile defense fit pretty well in a 5 minute set as well. At the top end, you have C rotations which you expect to take around 20 minutes, so it feels outside of the scope of the game to have to do 60 minutes. I'd rather it be broken up into 3 20 minute chunks.
3. Bounties - I don't like that the system encourages lower level bounties vs higher level ones. I think completing bounty segments would be better. 24 bounty segments would be 8 low level bounties or 5 high level bounties. I think that'd be a better system.
4. Without using life support - I don't like anything you can fail with a bad click.
5. 5 sorties - Since sorties are non-repeatable, I don't like the idea of something you can fail if you go on vacation for a weekend. Let's say I care about warframe more than going outside. Do I go on a vacation or do I do the five sorties? I'm going to pick sorties. That's bad for video game/life balance.
6. There's just a wild variance in difficulty between challenges of the same tier, and I think that's bad. 60 minute survival is way more demanding than 3 ESO waves.
Now, all that said, I think Nightwave is a great system that encourages people to do things that they should be doing anyway. In particular I love the Lua/Vault challenges this week. I haven't been able to make time for that kind of thing, and my wife needs mods from both of those. Generally, all the Nightwave stuff has fit into my playstyle (which is admittedly excessive) really nicely.