Fun and mechanically effective ARE two different things.
I like to think that Fun trumps Rules Lawyering every time. 
But be advised, many, many players would find being given a clearly mechanically inferior character to be "not fun." In fact, i think that someone who doesn't is in a small minority. Im all for RP. I like RP. I like a good story. I have been guiltyof more than my share of theme builds. But if you have new players, which this thread was about, and one has a character that is clearly mechanically inferior to everyone else at the table, odds are strongly in favor of him not likeing that. And when a game is just getting off the ground not liking often equals not coming back for more.
Also, mechanics should mimic story elements. Its hard to RP an elite covert operative if mechanically he isn't any better at his job than fred the mall cop.
Being good at the Game part of a game doesn't make you any less good at the Role Playing part of the game. Its not Rules Lawyering to build an effective character.
Its also a real pain in the rear for the GM to have radically differnt power levels in a group. A combat challenge that is good for one guy either murders the other or is not threat at all. Like I said above, the key thing is that no matter where the power level for the campaign shakes out to be you need to keep the characters roughly in the same range. This can sometimes be putting a cap on a power gamer, but in Shadowrun because its honestly so easy to make a flat bad character until you learn the rules a bit it is often making sure that the newbie does not completely stink up the place. All RP purity aside, a hacker who can't hacker, a fighter who can't fight, etc, is just not good for the game in any way. Its harder to GM, its harder for the other players who are relying on that character to cover his role.