I've got a B (and I've done a 50k on it, although I'm not sure I would have cared for much more) which I got after having a second-hand one stolen. I'm working through the Brompton "Bike Explorer" on their Website here.
The S-type handlebars are elegant, but the S-type front bag is tiny. Conversely, with M-type bars you can use the Touring Pannier, which is the largest and therefore the best, and accomodates a laptop bag and clothes/books/etc for a weekend readily. In a stiff headwind I crouch.
I have a 3-speed because that was what the bike shop had and I didn't want to wait forever for a new one. However, if I was getting one custom-made, I'd dither between 2-speed and singlespeed. Nothing wrong with the 3-speed, but the B doesn't really need a huge gear range for urban riding.
Mudguards (duh!). The rear rack, however, doesn't accomodate many normal panniers, and so is as useful as a chocolate fireguard. I've got a huge Carradice saddlebag which can augment the Touring Pannier - and unlike stuff strapped to the top of the rear rack, a saddlebag can stay on the bike when you fold it up.
I need the extended seatpost and I am only 5'10".
I like a B-17 Narrow, so I have another Brompton plastic saddle in my heap of useless saddles.
Brompton Yellow tyres are perfectly satisfactory.
The non-folding LH pedal is a false economy.
I fitted SONs to both Bromptons, and I cannot imagine doing without. The standard B dynamo headlight does not have a standlight; however, a B&M Lumotec Plus (_not_ Oval Plus) just fits under the luggage block using the bracket SJSC sell for fitting Schmidt headlights to a B - or if you are incredibly flush, I imagine a Schmidt Edelux would so fit (but don't buy one just on my say-so). I also have a Cateye 3xAA backup rear light which conveniently can be fitted to the top of the seatpost just above the saddle clamp.
My old B had Kool-Stop Salmons, and so will the new one when it gets through a set of brake pads.