I think I'll do the same. The two "takes" might be interesting.
The nova system needs a change of description IMO, given that regular stars can go nova, taking no time at all. Maybe change it's description to something like "the local star is trapped in a nova cycle, exploding, recondensing, and exploding again" and add some dangerous sectors. Also add an (invisible) star at the center, so it can be blown away.
Organic infestation- I'll change it's description so it's DEAD. Otherwise the thing would be trying to kill your ships!
Hmm. Maybe two varients- one alive, and doing damage in every square, the other dead. The alive one could have a captive sun at it's center, hidden, but enough to blow the infestation away if you can get a stellar manipulation ship in there. Or build a sphereworld around.. nautral defense
Red Giants- hmm. Probably add some asteroids near the outskirts, and some damaging storms in the star proper. Also an invisible star in the center, so you can blow it.
Green Giants- same as red giants. (BTW, reality speaking these things make no sense)
fragments- these are just plain WEIRD. hmm. maybe change it to an entire solar system. Would explain why they're so big- it got condensed down into a ball, then ended up passed through the other system, attracting all the planets in THAT system. Somehow avoiding igniting in the process.
Anamoly- look good as-is IMO.
Black holes- change description to "supermassive black holes" and remove the pulling-in matter thing, since they don't actually hurt any nearby systems. Maybe add some storms to the new pictured one, and make it pull at a speed of 1. You wouldn't actually see the hole.. and in SE4, you're not. You're seeing the crap that's on a decaying orbit INTO the hole.
Star forming: see nova and fragments.
Dead star: see fragments. The thing is *way* too big. Needs a description change.. hmm.
New nebulas: change description to be consistant with the old ones. Also change system type to nebula.