Jury is still out whether or not the sedan will get the 335i for the 2007 model year. BMW might keep it an exclusive for the coupe (most likely). No doubt, eventually the series sedan will get the 335i motor (probably an 08 model). BMW might however, decide to start the 08 model years early (March 2007) - BMW keeps doing this (starting the model year early) when they transition new engines into the line-up (E60 engine changeover comes to mind).

The 330i motor isn't going away. It's either going to become the mid-range model or the low range model. The N52 engine is here to stay. The next revision will have fuel injection - thats a couple years away.

Due to emission laws, the 2006 U.S. 3 series all share the same 3.0L engine. The 325i has different software combined with a single stage intake manifold and a couple minor hardware changes which reduce the power by 40hp. Therefore, they are essentially the exact same engine. In europe, the 325i is actually a 2.5l (which is able to pass emission tests i guess)...

Rumors do point however, that the current range will eventually end up with a 328i/335i. My guess is that will happen at the mid-cycle refresh point, where we will see the new N52 (N54 i believe, I'm not sure on the codename) based direct injection engines.

Optionwise, the 330i will eventually get nightvision, automatic headlights, etc... You won't be missing much, and these additions probably won't come until the E90 mid-cycle refresh at the earliest (again MY08 or 09).

So, I say go with the 330i. Unless you find that underpowered. In the worst case, the 335i will come out, and you'll be missing out on a new faster, albeit unreliable motor (BMW is going to take a while working out the kinks on this one).