As a system I think that charging is brilliant, it fits in with the games speed based turn based systems extremely well. As a matter of fact I think that having turns based on individual unit speed makes the vast majority of SRPGs that have player and enemy turns look somewhat juvenile.

In terms of balancing I think they could have done a better job on a few abilities. Some of the speeds on the really powerful magics are completely out to lunch, if a spell takes more than one turn to cast it better be ridiculously god-awfully powerful.* I think it is your dislike of the titles mechanics in general that has you painting this as a bad system, rather than one with a few questionable choices in balancing. Of course there is no argument that skills like Aim+20 and Meteor are rather useless abilities, but every RPG that I have ever played is chock full of useless abilities, aside from the ones that have a very restricted set of moves.

*Which could actually make an interesting mechanic if the risk-reward of casting a multiple turn spell was worth it in some cases. Wouldn't it be cool if you could actually cast Galaxy Stop but it just took a ton of MP and multiple turns to charge.