You keep saying that known mechanisms cannot produce new alleles, but the fact of the matter is that they do. This has been documented time and again. I did a search on Google Scholar for you, so feel free to check out the relevant literature:
"new alleles" - Google Scholar
Give this a read, too:
CB102: Mutations adding information
And for what it's worth, the genes that give rise to limbs in birds are the same that give rise to limbs in ALL tetrapods. They're called Hox genes, and they're universal among tetrapods. There's no reason to think things would be any different between birds and non-avian dinosaurs.
Why didn't creationism predict feathered dinosaurs? Because, once upon a time, YECs used to think "kinds" were these immutable groups of organisms that shared little in common. They were thought to be distinct so that features unique to one group would not be found in another. YECs even went so far as to argue that dinosaurs would never be found with feathers (as you yourself still seem to be questioning, judging from your hang-up with regards to "Archaeoraptor").
But now some YECs are coming to accept feathered dinosaurs for what they are. You'd think that would essentially do away with the concept of "kinds" since so many features are continuous across their supposed barriers, but that doesn't seem to be the case. YECs somehow still see this as consistent with the ex nihilo creation of "kinds", which suggests that there's really nothing that creationism doesn't expect to see (i.e., it predicts nothing concerning biodiversity; it is not science).
Microevolution is consistent with both YECism and evolutionary theory, so it cannot be used to distinguish between them, if that's what you're saying. Mind you, if you believe that there were only a few hundred different "kinds" on the ark and that all modern biodiversity radiated from those kinds within just a few thousand years, then you require a lot more than just microevolution to account for it. You'd need some sort of hyperevolutionary mechanism that is not known to operate today.
As for your questions about what science predicts:
1) Not sure what you're referring to about bee hives in the desert. Source?
2) Angiosperm spores have not been found in the pre-Cambrian fossil record. Evolutionary theory would predict that they should not be there. In fact, most creation scientists would be at a loss to explain them, too, given that they believe the Flood sorted organisms in part according to their ecology and angiosperms don't live at the bottom of the ocean. They know modern taxa aren't found in the oldest sediments.
3) No modern-day animal is the same species found in the fossil record. Coelacanths comprise dozens of species, only two of which remain today. And although they have changed relatively little since the Devonian, this is entirely in line with that we know about evolution. Evolutionary theory does not say that all organisms must evolve at the same rate. Some things evolve slowly, some quickly, depending on how quickly the environment changes. Aquatic environments tend to be buffered against the extreme changes seen in terrestrial environments, and so aquatic (particularly marine) fauna don't tend to change all that much if they don't have to.
Anyways, getting back to the point of this thread: Evolution predicted feathered dinosaurs, which are now being found in abundance. We can even determine the colour of the feathers based on the shapes of the preserved melanosomes. It's interesting that YECs are now grudgingly coming to accept that fact.
Anyways, I'm off for a vacation in the DR this weekend, so I likely won't be able to respond for another week or so.