Blame Activision. They won't give up the rights.

Since Microsoft owns Bethesda/Zenimax/Id now, can't Microsoft just buy these rights out from Activision?

Microsoft could, but apparently won't or can't.
I wonder if there are some legal issues, a la the NO One Lives FOrever Games, which keeps Activision from selling them.

Just because Microsoft has money doesn't mean they'll throw tons of it at Activision for this. Likewise, Activision may not want to sell.

Best thing to hope for is that id eventually tries to do something new with the series and that either gets talks going to bring everything under one roof or a deal that makes it worth Activision's while.

My opinion might be unpopular but I'd say that nothing valuable is actually missing.

Heretic II is actually quite enjoyable, though it's a 3rd person shooter rather than an FPS. The only downside to it is that the last few levels were a bit rushed and the difficulty drops off, especially if you dispose of all your spells and just slash stuff to hot salsa with your flaming murder stick.

Thank you for posting this as I was about to purchase it specifically for Praevus and was unsure if it actually was a complete Hexen series.