Well I'm not clear on what your goals are for this but you've obviously thought through the phonology.
Since this is an area I've also pondered somewhat, I'll just lay out all my thoughts:
I agree that the characters don't seem to flow well. Part of this, I think, is because you're attempting to adapt another writing system to English phonology rather than creaing an entirely new one. Certain shapes of glyphs, such as those for lingual plosives, appear so often that the script seems overloaded with loops and parallel vertical lines. There are also occasionally overly complex characters either because of ligature (transliteration for "rights") or phonological conceptualization (transliteration for "conscience"). Since the script is for a natural language, it would follow that the script would be illogical in various ways, that is, not so systematic. Though I enjoy logical scripts, it seems at least slightly out of place here. I suggest making an original writing system instead, with flaws in the correspondence between glyph structure and phonological structure of phonemes or a more concealed pattern for the structure so as to produce more variety in the appearances of glyphs.
A way to integrate the writing system into the show might be to assume that Canterlot has a separate script from that of Ponyville. In the first two episodes, when Spike is scribing on the parchment, he is shown writing in boustrophedon mode. In these instances, the script is never shown so it could be possible that the script shown in other episodes is separate from that of the first two since subsequent episodes show the script written from left to right and Spike and Twilight could have assimilated into the linguistic culture of Ponyville by that point. Such a scenario would allow for a great deal of creativity while still agreeing with what's shown in the series.
(and I've also been building up the will-power to create an algorithm for "deciphering" the script that's actually been shown)
Partly because of preference and partly because of evidence from the show, I suggest the script be cursive only.
Anyway, just some ideas. I don't know where you want to go with it but I figure since I seem to be the only other brony on MLP Forums with any interest in the area, I'd share my opinion.