Thinking at light-speed does not equal to intelligence. In theory, it sounds excellent. Since he thinks at light-speed, he can gather intelligence faster than the most advanced computers in DC universe. Unfortunately, stats on a sheet don't mean anything if the stats aren't applied to and shown by the character. For example, in theory, Killer Croc should be able to lift more than ten tons and take shotgun blasts to the face but loses to Harvey Dent and various policemen. When has Superman ever demonstrated genius-level intelligence on par with Lex Luthor? If Superman was more intelligent than Lex Luthor, Lex Luthor wouldn't be a challenge to Superman. It's the same concept with the Flash. If Flash is more intelligent than Lex Luthor, he could solve every crime easily, cure ever disease ever, and stop millions of deaths. In fact, since he reacts in septoseconds, why doesn't he stop crime in general? The fact is that this is the comic industry and that stats are thrown around for the purpose of sales. Without any proof that Superman and the Flash are more intelligent than Lex Luthor, then Lex Luthor clearly demonstrates a superior intellect over Superman and the Flash.
In Red Son, Lex Luthor is stated to be a 9th level intellect. In the New 52, Jor-El is stated to be an 8th level intellect. Jor-El was possibly the most intelligent Kryptonian in a far more advanced civilization. Also, keep in mind that Jor-El has never had the ability to think at light-speed since Krypton has a red sun.
As for my second question, if you want to have an unjustified opinion, you can throw yourself a party. At the end of the day, you haven't given a single reason why Batman is mentioned alongside Lex Luthor, probably the most intelligent human in DC history. In fact, he's the only human beings like Darkseid and Brainiac even bother to deal with.