Twilight B4 morale buildings not auto upgrading

I think it's intended that this doesn't happen, but I do wish it would, or that we had more ways to manage planetary improvements:

Like a governor that lets us upgrade all buildings of a certain type to another building of a certain type, for example. There's other suggestions in other threads here on this same topic.

Also, Dratha temples and media centers don't upgrade to healing pools.

Is this just for those morale buildings? Do other buildings auto-upgrade?

Buildings have an upgrade path, I think, rather than an automatic "buildings of X type autoupgrade to superior buildings of the same type." So Healing Pools will upgrade to Wellness Falls, but Dratha Temples will not upgrade to Healing Pools. Similarly, Improved Factories won't upgrade to Thalan-style factories or Drengin slave pits or vice versa.

I do recall seeing research buildings auto upgrade into Neutrality Learning Centers, though.

That's because Discovery Spheres auto upgrade to Neutrality Learning Centers.

Sometimes it won't auto-upgrade to NLCs. Very rare occurrence, but I've seen it happen.

As Phaedyme said, the Media Centers are hard-coded to upgrade into

Yes, it would. I really hope such a feature makes it into 2.0.

The current setup is manageable - at least, it was for me with Altarians when I picked up the entire Healing Pools path of techs and left Media Centers and Dratha Temples behind forever. With regards to Altarians, I wish they'd just have one path to specialize in, because without tech trading they're screwed.