"Third smartest man" is a dumb nickname, for a really cool character. It should be to impossible to say whether Mister Terrific is smarter than Lex Luthor or vice versa. It should just be obvious that they're both six-sigma out from the rest of us. Including Batman.
The story that converted Wonder Girl into Troia was actually pretty good. If they had done it with Lilith or a totally new character, it would have worked.