First let me say I agree w/not being a fan of the S as a Kryptonian symbol. It's such a superficial attempt to ascribe some "deep" meaning to the symbol, but only comes off as either too coincidental or contrived when you think about it. Although when it comes to him having the name because of a career as Superboy, I don't see that ever working on the big screen, not because of anything inherently wrong w/the idea of Superboy, but just because the meager amount of time you'd be able to spend on Superboy in a SuperMAN film doesn't justify it. The concept works much better in the comics where you can delve into it every month. In a two-hour movie it would seem just thrown in "just cause". Much better to just focus on him becoming Superman as an adult, which by all indications they are going for in this new film. Given that, I'm personally a fan of Lois naming him that in the papers. Now I'd imagine that you(Pre-Crisis purist that you are) probably won't agree w/this but, while I hope for the characterization of Superman himself to lean more towards Pre-C , I still think that Byrne's version of his first public appearance was great, where he saves the space shuttle in just regular civilian clothes, leading to Lois naming him a "Mysterious Superman" not because of seeing an S on his chest, but because that's what he IS... a superman. If they MUST have some Kryptonian connection to the symbol, I'd prefer the Kryptonian symbol to be this....
.......and then have Clark reinterpret it into the S symbol in order to "make it his own" AND to go with the name Superman that the press and public have taken to calling him. My own idea on how he'd do that is that this....
......would be either the logo for Smallville High's lettermen's jacket's or it would be the lettering used on the "Welcome to Smallville" sign on the edge of town, hence Clark combines both of his heritages into his own, new insignia....the S we all know and love. But alas, since it has become the new standard since STM, the reboot will probably just default back to the S itself as the El family crest idea.