Hi, I have a 2001 Giant TCR-2 from new (9 speed 105; Mavic CXP21; ONCE team colours) and a 2005 Giant TCR C-1 (original spec: full 10 speed Ultegra; Mavic Ksyrium Elite) also from new.
When I bought the TCR C-1, I was expecting better times around my routes but no such considerable thing! Did that disappoint me? Only in part... I was marginally faster but the biggest and definitely worthwhile gain of moving from ALUXX to carbon was ride comfort (more compliant) and handling (sharper). Ironically, after road accident damage now I'm back on the TCR-2 and missing the C-1.
Over the years, I upgraded the C-1 to keep it current and improved it with full Dura-Ace 7800 (including CL24 wheels) and Giant Racing Components (lighter carbon h/bar to match the original stem plus seatpost vs the standard Giant bits) and that absolutely transformed the bike. Great in sprinting and going up, around 7.5kg with lots of accessories stuck on it.
I can't comment on 6500 to 6600, except to say the 105 5500 has been bullet-proof compared to the original 6600 which was a bit niggly. Going to 7800 was heavenly instead... except for the higher cost of components.
I am confused on why your TCR-0 has 6500 (it had full DA along with a carbon steerer and ONCE team frame imprint) and why the C1 you refer to is a 6600/DA mix (the silver one you linked is actually the TCR Composite Euro with Campagnolo Centaur). My blue C1 had full 6600 (again, carbon steerer) except for the FSA crankset... disliked and upgraded the Gossamer to a new (and luckily colour matching) Team Issue from a 2004 TCR Composite, and then fancier FSA chainrings around 2 years ago.
Anyway, I can't really comment on Shimano v FSA crankset either... I would describe the 105 5500 as frail... but I never had any problem with the FSA Team Issue (higher spec to Gossamer), so much so that I will soon have a new DA 7900 bike with an FSA K-Force Light crankset (also a team issue component).
Good luck with deciding and below is what my C1 ended up looking vs an original catalogue spec:
