+1 on the depreciation. Within days of driving off the dealer lot, you've lost a good 15% off your cash. Unless you can find a killer incentive on the outgoing model. Also keep in mind the more complex a car is, the more it will cost in upkeep. The 335i does have more tech wizardry than the 328i but there are more things to cost you down the line (if you intend to keep the car past warranty). Not saying that's a showstopper, but just something to be aware about.
As far as the transmission goes, it used to be that automatics were inferior on shift speeds and fuel economy. But the new crop of automatics equal or surpass the manuals in both areas, thanks to advancements in control algorithms. But BMW is probably one of the last remaining OEMs putting out high quality state-of-the-art manual trannies as manistream. A few years down the line, manuals may not exist anymore when EVs and hybrids proliferate. Something to consider, especially if you are the sporty kind of driver which it seems like you are... Personally, I am a firm believer in manuals and every car I've owned has been a manual.
I would also recommend the Sport Package in whatever you're getting. It comes with better front seats and a slightly lowered, stiffer suspension than stock.