I think the ToE's biggest challenge is that it cannot explain how life on earth began.
Are you aware that it does not even have a reason to try?
There is considerable speculation and progress in research about abiogenesis, but that is unrelated to the ToE.
I suppose you may be confusing matters because neither the ToE nor abiogenesis research make a point of decreeing the existence of a designer.
In any case, why would a matter that does not concern it at all be a challenge to the ToE?
To claim to know how life's diversity appeared without knowing it's beginning is, to me at least, simply bluster;
Well, that sounds at least a bit arrogant and naive, I must say.
It is akin to saying that to claim to know how chemicals react without knowing who or what created matter is "bluster".
People
can learn and teach useful things without claiming to have the primordial answers, you know.
which is why, I believe, evolutions advocates try to sweep the dust under the rug of abiogenesis.
Why would we even need or want to do something that is ready-made in the first place? The ToE
does not even attempt to explain the origin of life. It is a fact.
It is certainly compatible with abiogenesis, which to some extent is a natural hypothesis to develop from it. But you are really grasping at straws in attempting to discredit the ToE by proxy like that. It makes you sound like you have no idea whatsoever of what you are talking about.
Second: IMO, the fossil evidence does not support the gradual evolution of life, despite endless and at times fraudulent attempts to make it appear to do so.
Well, what about the facts then? Not only the fossil evidence, which you are basically saying that you don't want to learn about, but also the biological evidence of several kinds?
Third: There is, to me at least, abundant evidence of a surpassing intelligence manifest in the evident design and structure of living creatures.
We get that you are a Theist. Fine. But a poor reason for fearing the truth.
There is no compelling evidence that such intelligence is simply the manifest destiny created by the environment or biological necessity.
I agree. There is no manifest destiny, far as anyone can truly tell. Evolution is aimless, although the selective pressure of the environment (an abstract yet useful concept) does lend it very circunstantial aims along time.
Oh, and there is no compelling evidence that this intelligence you speak of exists, either.
There are more holes but these three are sufficient to bury the ToE.
Except that they fail utterly and spectacularly in even addressing it at all.