The way I see it, the first 4 seasons and the lost season are triumphs by themselves. It is the ultimate SatAM cartoon, telling intelligent, yet straightforward storytelling, but also carefully balancing action/drama with character development while letting Mikey handle comic relief. TMNT 2003 is one of the few SatAM cartoons that truly enthralled me (which shamelessly includes the "filler" Orihalcos YGO season).
I view FF as an abomination but I do feel that BTTS let the show return to its roots some. However, if the DTV does not end on a reasonable note I'll simply treat FF and BTTS as bonus episodes, rather than part of the continuity.
I'm sure at some point the show will be rebooted down the line the way YGO, Gundam, He-Man, and GI Joe always are, but until then, TMNT 2003, which lasted seasons upon seasons of episodes (the first two seasons alone constituted 52 episodes overall) is a stellar example of how you make a good action/adventure cartoon, PERIOD. It is the Turn A Gundam of American cartoons, a classic, but it won't be appreciated until years after its conclusion.