Malachor V was a horrible design, I agree. I couldnt but feel like it was a level right out of Hexen. Personally, I would have done something far more ominous if I were in charge of the level design. I probably would have had it be a MASSIVE valley (think grand canyon in depth and width of the canyon) with the area beneath expelling the green aura we could see from orbit, while you could have a CLEAR view of a rampaging storm above.
At the mouth of the canyon would have been the temple, and the whole world would have felt like a world both dark and ominous, and very very dead.
Such an area like along the side of canyon would have been good for a final confrontation between Hannaar and Mira, as when Hannarr is defeated, he is hanging onto the edge of the cliff, and Mira could have tried to save him only to have him be overcome with the idea of having to serve the lifedebt again and choose to just fall (similar to luke in Empire Strikes Back) or if you are playing Hannarr, he could have simply defeated her, and thrown her into the canyon, like the Emperor's fate in RotJ. (recreating moments like those in star wars is important
I have to say, Peragus was very good level design also. I thought Telos was OK, though I would have rearranged it so Czerka, Exchange, Cantina, Ithorian, Medical Center, Shop, and TSF would have been in one large "hub" sector, a residence sector, and then the docking sector.
Dantooine was well balanced, but my favorite planet had to be Onderon. The spaceport could have been made to feel more like a spaceport, but the city was well designed I think. I just wish there had been a couple more areas to it (like a residential area or more of a "market" feel to the center of the city) and some more quests definatly.