Brakes - yes they are not the best. I replaced my front brake lever with Avid SD-7 I adjusted it so max hand force was just before the lever gets to the handlebar so max force and max control. The tight bend in the brake is a big part of the problem. If you only ride Bromptons you adjust via more force.
Luggage is excellent, I cut handle off the stock C-bag frame and replaced with shoelace weaved handle, so the handle does not foul the brake levers. The C-bag is ample space for all I need, e.g. can go camping with it in summer.
Bottle cages, agreed, but you can put a main-tube velcro-strap type thing on and carry bike via saddle, only a 0.6L size though. Unfolded you can put them all over the place. For short rides I have 0.5L in C-bag rear pocket, longer rides I can fit bottles on the seatpost and the front stem. The pannier can carry pouch to top-up or instead of bottle but bottles easier to carrry.
Cramped? Well if you push the saddle all the way back, flip the pentaclip so its front of the saddle, it can go welllll back. The S-bars need a longer model (newer or replacement)
Flexing, well with S-bars there is very little flexing. Are you suffering from some play in the steering or brakes and need to adjust? I also have a Brooks Switft which is stiff saddle but shaped to my contours so comfortable and I replaced with stiffened suspension. I don't find it flexing.
I have S6L-X the older 6-speed with 6 close-gears and I customised front gearing, either a manual-move double-chainring when I'm generally in flat areas or I swap for Mountain Drive Brompton model which self-fits easily, if I need to go through a long undulating route.
I used Ergon grips to compensate for the harsh hand shocks from S-bars that solves the issues but my next modification is a longer S-bars, its cramped on the bars between grips and gear shifters but I have the 2007-model with shorter bar than newer model (48cm vs 51cm).