I got my Brompton for a great price used, so I didn't get to choose the configuration.
I'd definitely go from three gears to six. I want the bigger gear range and and greater versatility, and less worry about hills. For a while, the Brompton was my only bike, and that felt like a real limitation. But now I have a second folder, with bigger wheels, lots of gears, and a wide gear range, so the gearing on the Brompton matters less to me. I now have a bike more suited to long, potentially hilly rides, and the B is more of an around town bike.
I might want S bars instead of M bars, but I'd want to do more test riding to decide. I also would be thrilled about having to use an S bag rather than the bigger C bag.
I Might add a rack, but I'd also want to try it out to see how much it matters to me in real life, in terms of rolling and what it can carry. Weight matters to me, because I have to schlep the thing up four flights of stairs.
I thought about upgrading the Brompton, but ended up buying a Tern instead, and the two bike combo works out pretty well for me, so I no longer feel much of a need to change. It would be nice to upgrade my B, but I'm not made of money.