I made the move from a 2006 3.0si to a 2010 35is 3 months ago - here is my take on it.
3.0si - loved it. Seemed small, great interior, very quick & agile. The only problem was that I looked at a e89 a few months after I bought the e85 & it ruined it for me.
The e89 just seemed so much nicer inside (where you spend all your time) so I test drove one & that put the last nail into the e85 & it had to go.
The 35is isn't quite as 'alive & agile' as the 3.0si, but leagues ahead in the interior quality. Overall performance is on another level - it feels genuinely much much faster with a huge shove in the back (where the e85 was more of a wind up to the performance rather than instant).
The metal roof is overall much better - the pluses being the better isolation & solidity with it up & the overall coupe type look, but it is a pain in the arse having to take up so much boot space with it down. Overall I'm happier with the metal than the cloth, so all good.
The e89 has all the modern bits that I was missing from the e85 - Bluetooth, decent nav (idrive), heated steering wheel - just feels like a more modern vehicle.
Fuel consumption is worse on the 35is (by a long way). I was averaging around 34mpg (75% city / 25% motorway) on the 3.0si, with the same mix of driving I only get about 26mpg from the 35is. Not great, but I put up with it because the overall experience is just so much better.
I was looking forward to the paddle shift - but on a 2010 car they are very disappointing (push /pull change on both sides). The feel was... 'clicky'... and just not intuitive. Easily changed for the shifters from a 2012 car (same as on theM3 I believe) so just pull/pull one side does down, one side does up. Then it is perfect.
The combination of DCT with the adaptive suspension (standard on a 35is) makes it a real jeckle & hyde car. Fast at all times, but can be comfy & smooth with a real blatant step up to a more aggressive ride & become a proper 'play car' when in sport plus, shifting with the paddles. On a lot of cars the change is subtle - on the 35is it is like having a completely different car. Brilliant & super flexible.
The noise from 35is is really addictive - very rorty exhaust note that is quiet when pootling around town, but you can provoke a lot of noise very easily. I love it. Get the roof down & it is a great experience all by itself.
I think the bottom line is that you need to drive a 35is if you are considering the switch. It will immediately clarify which you prefer & for me it completely ruined the e85 experience & I changed straight away & have not regretted it. There is no other car I would switch to under £50k (second hand budget for me) & that says a lot!
Matt