It was an option... the 6-speed manual was the standard transmission (but didn't get ordered much by dealers who know that it's easier to sell an automatic).
As for tuning, you'd be far better off with the N54 if you want to tune the car at all. The N55 has some tunes available but there's not as many options and you won't get as much power out of them. I think the general consensus is that the N55 is a really good engine but it's harder to find gains than with the N54, partly because of the systems integration and partly because of the engineering differences. But if you're a two-pedal kind of guy then the N54 135i comes with a traditional automatic rather than a DCT.
I have to say that I drive a DCT because of some health problems last year (knee surgery)... but as it has healed now to the point that it's almost back to the way it felt before (or better) I am starting to miss that third pedal. I can't help but think my next car will have three. That's not to say I dislike the DCT; from a technological perspective it's phenomenal... and for the driver it is absolutely wonderful with faster shifts than I could ever manage. It has a few "bad habits" that you learn pretty quickly to work around... and once you do there's not a lot of other cars in the same power class that can keep up with you.
2001 E46 BMW 330i Sport Package 6MT
2004 BMW R1150GS
2004 E60 BMW 545i Sport 6MT
2012 BMW 135i - Deep Sea Blue / Terracotta / DCT
2012 BMW K1600GT - Vermillion Red Metallic
2008 BMW E90 M3 - Interlagos Blue / Silver / 6MT
Last edited by thumper_330; 12-12-2012 at 08:13 AM.