They switched character designer for a reason 
, she hasn't been lead since 2005. Low IQ I agree with, for Kanon certainly, Nayuki (she's just a ditz), Ayu and Makoto are all dopey as anything. Be it for the later two there is reason, and you are suposed to realise something is up. Shiori, Kaori, Sayuri and Mai don't have that problem. Every route has a character with a mental problem in it, mostly depressive withdrawal; a few having messed up IQ seems right in that context.
Having characters speak differntly helps distinguish the speaker, remeber it's originaly text based, especially in the flashback/dream bits where it's the only way you can tell who's speaking. Same way manga write characters in different font, or use differnt styles of speach bubble for differnt people in conversation.
It's only realy Kanon that has that problem. Clannad has some of the cleaverest (or at least academic) female characters in it. Most of them have a degree (at least) post timeskip in afterstory. Only Fuko acts childish, and she has realistic problems (not the astral projection bit, the messed up social interactions etc. her sister talks about).
The shows I mentioned are all most definatly moe shows as well. How the hell is A's not moe the bad guy is [spoilerinline]a wheelchair bound terminaly ill grade schooler, or a pair of catgirls[/spoilerinline] for hecks sake, also crazy high Saimoe rankings.
