Some of your suggestions have merit; the 747 would probably benefit from a blade tailcone and a composite stabilizer. What's the point of your list, though? Realistically -- and I say this as someone who dearly loves the 747, grew up crossing the Atlantic in -100s, and generally admires Boeing -- the 747 is nearly obsolete, and further investment in it is probably a waste of Boeing's time and money. Even if one called your list of changes modest, it would still be a multi-billion-dollar investment in a product that has only niche appeal, based on a 45-year-old design. Redesigning the entire flap system, and the fairings, and the spoilers? That's a huge amount of work, before we even address the stringers and other fuselage changes. Too many structural changes, and it might need to be re-certified as a new type by the FAA, and it wouldn't pass that without major reworking (the L1 and R1 doors would need to be moved, just for a start).
The plane is compromised by the upper deck geometry (narrow and with a low ceiling). It creates a more exclusive environment, yes, but still imposes weight penalties. If you stretch the upper deck further, range will decrease. As it is, Emirates didn't want the -8I in the 220" stretch because they wanted more range, not less. I'm not sure if any substantial stretch of the upper deck would be balanced by your weight-reduction suggestions. Reducing range further for a marginal increase in capacity is a losing game even before you consider the effect on aerodynamics of moving the hump further aft of STA 1241. Plus, much more stretching and you'd need a new emergency exit, depending on seating configuration. If you're talking about stretching just the upper deck, then baggage for those passengers would have to be stowed in the extant holds, eating into revenue cargo space. If you're talking about three-deck fuselage plugs, then Joe Sutter would tell you that a further stretch of the airframe is likely to require a new wing. The location of the flight deck on the upper deck also makes handling a bit trickier; pilots learn it, of course, but it's more challenging.
The market is clearly skeptical of the 747, too. There have been 261 airline orders for the A380-800; only 31 copies of the 747-8I have been ordered by four airlines. Most of the carriers that bought 747-400s have passed on the new variant. As a freighter, the 747 is still very useful (with 67 orders), and 9 more have been ordered as VIP aircraft. As a passenger carrier, it's just well past its prime. The A380 carries more people, with more space. The 777-9X looks poised to squeeze it from below, with 407 seats and better fuel economy. There's still a market for a plane in the 747-8 size class, but it's very small.
At this point, Boeing would probably see better results by putting its money into a true high-capacity 747 successor and/or A380 competitor, something like the '90s NLA or LAPD studies, or something a bit smaller, size in the authentic 450-seat range, but with 2 or 3 engines (a modern MD-12 Twin, in essence). Boeing is more likely, I think, to take the second approach; their statements clearly suggest that they don't think there's room for the A380 and a direct rival, and they don't want to repeat the DC-10/L-1011 debacle. Obviously, this is just an offhand armchair analysis, but I can't see incremental improvements of the existing design netting Boeing much in the way of new business anymore.
