I'm such a big fan of the Megara. They're realized quite cheaply, but they look impressive, their bureaucratic nature is amusing, and they are truly some of the most unorthodox aliens seen in the series. Most aliens, even the most ambitious attempts to create something different, such as the Zarbi and the Menoptra, still look like men wearing suits. The Megara are entirely unlike anything seen in the series, and even their speech between themselves is incredibly bizarre.
The trial sequence where The Doctor appeals for his life whilst trying to expose Vivien Fay for who she is seems worlds away (literally, almost) from the mood and theme set up in the first two episodes. This is not necessarily a bad thing, though, although it does make the story seem like an amalgam of a pair of two-part stories. Only Doctor Who, however, could make such a staggering switch in tone and setting and get away with it.
Like The Pirate Planet before it, though, the Key to Time segment is given little attention and seems almost like a Draft 4 afterthought. The Stones of Blood is far from perfect, but is so entertaining to watch that any little faults (like why The Doctor has a lawyer's wig in his pocket for just such a scenario where he's having to defend himself in a court of law) fall by the wayside and don't effect the overall enjoyment of the story.