One, I find it highly unlikely that these huge, awesome birds would change into the pathetic Cuccos.
I find it hard to believe that
any race such as the one Shad describes would "change into the pathetic Cuccos." Either the Oocca are not as pathetic as you think, there was some external reason for it (like in the case with Zora->Rito), or the Oocca are
not the advanced "sky people" that Shad and Ooccoo claim them to be.
Second, there's not enough time in-between SS and OoT for that kind of evolution.
How can you say that? You have no idea how much time there is between the two games. Even so, the Zora 'evolved' into the Rito nearly instantly during the flood, so time is shown not to matter.
My current theory, which will likely be disproved in SS (my previous one regarding the Oocca was), revolves around Ooccoo not being entirely straightforward. It also involves the Japanese text, which I'm told has no mention of "Oocca", only "sky people". In short, the birds in TP are not the great sky people. Yes, I agree with the OP, they could be the Loftwings. The sky people would then be the Skyloftians.
However, I don't hold on to this theory very strongly - it has many holes. Not only does it just not seem right, but much of it depends on how SS's story plays out. So far, not much of its story has shown congruence with what we know (or think we know) about the Oocca or the sky people.