The current missability of Alert rewards, particularly Nitain, is absolutely a huge frustration and I welcome the move away.
With that said, I'm concerned that this promotes burnout. The current alert system offers the following:
(Virtually) guaranteed grouping. I don't think I've ever done an alert, even for only Credits, and not had at least one other person not matched in before I left the spawn room. But for Faction dailies etc, doing them at an off-peak time has often left me running solo.
Monotony breaks. Seeing a random Kubrow egg or whatever come up will often get me to switch tasks, and alleviate the boredom of grinding through dailies.
Bite-sized gameplay. Related to the above, there's a ton of grind in Warframe. Alerts, by their nature, cannot be effectively 'ground,' and so help mitigate burnout.
The new system furthers a "thanksgiving" style gameplay -- an eat-till-you're-sick buffet. My hope is for you to counterbalance this somehow, and not dive to deeply into the daily chore cycle in an attempt to solve other problems.