OK I changed those you mentioned. Those were some I wasn't so sure about. My campaigns didn't take my players to those regions and they (and I) did little research regarding them.
Hinterlands: I won't use this civ for every scenario, but they are useful since Thyatis has never conquered their entire nation, just 1 tribe capitol. The tribe has moved it's capitol and the other 3 tribes still fight as well.
Norwald: Same as Hinterlands, it is ruled and fought over by Thyatis and Alphatia most of the time, but in my campaigns, the people rose up after the War of Wrath that broke both of those empires strength and they gained independence from the larger empires. Norwald was finally united.
Savage Baronies: I understand the importance of this region, but I'm not too particular on city-states being seperate. A corrupt style government can make it seem that the Barons fight and argue a lot. I'm not sure the real importance of the City-States other than the only source of cinnabar on Mystara.
I can't get rid of Malpheggi because I need civs for Davania. Also this civ is one of the more dangerous "evil" civs that existed in my campaigns. The remnants of the Temple of the Frog. In fact I am changing part of that past and making them ruled by a Draconian (which don't exist on Mystara as far as I know) who found himself a one-way portal from Krynn. As a general in the armies of Queen Takhisis he learned to rule with an iron fist and was dismayed to discover the reptilian races of Mystara had fallen into barbarianism. He discovers an ancient temple in Brun and takes the relics away to a more remote region. He ends up in the Malpheggi marshes near Darokin and begins enlisting the Lizardmen there. They take to the teachings of the Temple of the Frog and he soon has a strong army. He raids a nearby town in Darokin called Athenos. As he makes plans to invade further, the full strength of Darokin comes down on him and so does a surprising army of Halflings form the Five Shires. (My characters had a hand in all that.) They were not able to defend the city well, so The Draconian named Xargass commanded his army to take the ships in the harbor and flee to the ocean. They did and the few who survived found a remote region in Davania and begin to rebuild there. The frog peoples and more Lizardmen of Davania soon joined under the command of Xargass. Does this seem far fetched? It is because the Immortal Ka (who loves unique races) wants to preserve this new nation and see what will become of it. He made sure enough survived the trip and even allowed winds to speed their journey and allow them to escape Darokin's small navy.
I've been thinking of Ochalea and as far as history I'm aware of they were always under the control of Alphatia or Thyatis. Maybe in a post War of Wrath scenario (which I'm considering now) they will have freedom and be a seperate civ. If I do this scenario, I will throw them in there.
My biggest problem is that I can't pt more than 31 per scenario.

I wish I could put 60 and then I would be more satisfied. Maybe Civ 4.
P.S.-I adjusted the ones you thought were different in the earlier post above. I agreed with you.