I went from a 23i auto to a 35i manual a couple of years ago. I liked the 23i a lot, it was a nice car and went well - but...
the 35i is awesome. I always thought that if I was going to have a BMW, it had to be a straight 6, and personally I feel that a manual is more involving, although the 6 speed auto is very good. I have never driven a car with the DCT.
I have not had any problems with mine, changed the runflats for Goodyear Eagle 3s, which made the car so much nicer, and new pads etc.
As they're both 6 cyls, servicing costs won't be radically different, and 30+ mpg is easily doable on a run.
The 35is does have the adaptive damping, which is pricey to fix, and I think you have to get BMW to fix it if you do have problems, and the 35i/35is both have potential HPFP and turbo issues, although if you are looking at a 2009/10 model, these will probably have surfaced already by now.
Insurance/Road Tax is a little more, but not a lot more, they're not in the £500+ pa bracket for road tax, mine was £305 last year, and I think my insurance was an extra £20-30 a year.
Man maths aside, the 35i is a great car, I don't regret changing from the 23i.
Best of luck with your decision.
Cheers, Dave