The fueling problems seem mostly resolved by the latest ECU software, which can be field installed by the dealer. Most of the reviews (both US and abroad) complaining about fueling were done before the 7.0 version was released.
The transmission failures are worrisome, but the total number reported on the various forums is fairly small -- maybe 8-15, depending on how you count/classify them.
There's always the issue of "selection bias", which is users experiencing problems are more likely to report than those not. OTOH, the total production run of K1200S bikes is likely tiny next to Japanese sport bikes, so as a % of the production, the # of failures are likely quite high. If the same % of GSXRs had transmission failures, those boards would be clogged with reports, and they're not.
On my '06 K1200S, 7.0 fixed most (though not all) of the fueling problems. My transmission failed at 7,500 miles, fully replaced under warranty.
You get used to the clunky shifting, certain techniques can mitigate it. It's just 1-3, not 4-6. Don't know why it's that way, maybe because BMW used straight-cut (not helical-cut) gears. Straight cut gears are stronger for a given size, alternatively allowing a more compact gearbox for a given load factor. However they don't shift as smoothly. If that was the decision process, it seems a poor tradeoff, as shift feel is a key tactile quality impression customers get on every ride. Just speculating here.
Do I wish these issues never existed? Yes. IMO it was an idiotic BMW management decision to release the K1200S in its initial state, then pull it from the market, then have to release several software fixes to achieve true production quality.
If there was another bike close to the K1200S features and capability, I'd have considered that, but unfortunately there's not. Honda quit making the Blackbird, Hayabusa is chain drive, no factory luggage and no ABS, ditto the ZX-14, VFR is underpowered (relative to KS), new Kawasaki Concours 1400 (1400 GTR) looks interesting but isn't available yet.
The KS ABS and ESA systems are great, dealer experience is a cut above some Japanese dealers who also sell ATVs, chain saws and personal watercraft. However BMW had better not rest, as the competition is continuously improving. Prematurely releasing an unfinished product gains a few sales but hurts the product and company reputation, which can take years to undo. I hope BMW learned from that.
In general the K1200S is a great bike, fortunately most of the serious problems seem fixed or understood. If I was buying again today, I'd still get the K1200S, as there's no close alternative, depending on how you weigh the importance of various features.
If Honda ever does an upgraded VFR literbike or Kawasaki puts ABS on the ZX-14 (in the US) or the Concours 1400 turns out well, those might be future alternatives.