In terms of spec, I would suggest having a look at the list of possible extras and deciding which are important to you. Most on here will say heated seats are essential, but if you're only going to put the roof down in warm weather then they really aren't important at all. My first E89 had absolutely no added extras, but it was a manual 30i which was exactly what I wanted - there wasn't a single moment when I missed iDrive, cruise control, heated seats, PDC or anything else.
My current E89 has most optional extras, but that's just because they happened to be on the first well-looked-after, sensible mileage, post-LCI, Orange 35is I came across. The only extras I would miss are the higher spec sound system (important if you want to listen to music with the roof down on the motorway) and the heated seats (I like to have the roof down any time it isn't raining).
My personal opinion is that this is the kind of car you buy with your heart not your head, so prioritise whatever spec/engine/colour that will make you smile the most (or lack of which will make you angry - i.e. PDC if you're sh!te at parking!).
They're both brilliant cars, although IMHO the manual transmission is rubbish - otherwise I would have gone for a manual 35i instead of a 35is. The DCT transmission is brilliant coupled with that engine and the 35is exhaust. If I sold the 35is and bought a 35i, I would probably have to spend a couple of grand on a new exhaust to make it as fun to drive. The 35is, I believe, also has bigger brakes and tweaked suspension that sits a bit lower than the 35i.