I'm glad you enjoyed most of it.
I think you're being a bit harsh on South East London however. I really enjoyed most of the walk east from Tower Bridge to Greenwich. You have the beautifully restored old brick wharves and cobbled streets around Butlers Wharf, just beyond Tower Bridge, which is my favourite part.
Then Rotherhithe too I found full of character, with more old wharves, cobbled streets and traditional boozers, with the added interest of the Brunel Museum, too. It opened my eyes to an area I knew little about and had never considered visiting before.
Beyond Rotherhithe there are some grim parts I'll agree though also some places of interest such as Greenland Dock, which I quite enjoyed. Then you have Greenwich which I loved. The Cutty Sark yes, but well worth walking up the hill to the observatory too, where you have a wonderful view. Much of Greenwich is a World Heritage site, so I think to miss that out would be a real shame.
Beyond that, well I mostly agree with your assessment. The millennium dome/O2 or whatever it's called now is worth a quick look (though the view from the Thames path is mostly through a high metal fence, so not great), and the flood barrier also quite interesting to see. Though I'd go down to the north side of the Thames and see it from Thames Barrier Park (right beside a Pontoon Dock DLR station). If you are on the south side, the walk from the Thames Barrier to Charlton is seriously grim and I'd very much like not to do that again! So yes beyond Greenwich hop on the tube to the dome and the barrier and don't bother with the walk would be my suggestion too (but I think the bit from Tower Bridge to Greenwich is well worth doing).