To me gradualism is difficult to imagine as explaining everything.
That's OK. Nobody is asking you to imagine gradualism. The evidence shows that the rates of changes in populations changes tends to be that of periods of stasis followed by relatively short bursts of rapid change. The theory backs this up.
The fossil of any living thing found is no garuantee that the creature had any offspring at all. How do I know that animal was the ancestor to another ?
You don't. But we can say that the population of organisms (animal or otherwise) that the fossilized organism was part of was either directly ancestral to x or was closely related to a population of organisms that was ancestral to x.
If you want to know how we know that, that's a topic for a completely different thread.
And it most mutations are said to be destructive and harmful and the minority of lucky ones are helpful, why don't we see many fold more fossils of the harmfully effected organisms.
How do you know you haven't seen such a fossil? Did you compare the members of the population that particular organism was part of and their differential reproductive success in the environment they lived in (including all genetic effects, as well as other organisms)?
Since you can't observe it directly, that's the kind of work you have in front of you to reach the conclusion you imply here.
As a more general answer: when it comes to terrestrial vertebrates there really aren't that many fossils. By probability the kinds of things that fossilize were things with large populations and they got that way by being pretty good at what they do. And so the handful of examples we might have of them will show us this. Grotesque mutants simply don't get born/hatch.
I suggest you look at marine life: molluscs have left a lot of fossils. You might develop a method for indirectly comparing relative fitness in at least one dimension and then you'll find your 'harmful' variants.
To believe that evolutionary gradualism accounts for all the life that we see there has to have been some ability to intelligently look ahead - ie. a plan.
But we know that evolutionary algorithms can quite happily exceed even our expectations and do better than any plan that we can produce. So why do emphatically believe there must necessarily have been a plan?
What do we lose by admiting that a Creating God is vastly more smart than we at this time? Do we lose the initiative to study science? I don't think so.
We lose nothing. However, if we are in pursuit of truth it would be wise not to automatically assume that the God has forethought. "Evolution is smarter than you." is a refrain you'll find little disagreement with in biology circles. So sure, we can assume that the creator of life as we know it is smarter than we are. I see no reason to assume it has a personality... as far as we can tell only organisms with evolved brains have personality.
Aside from humbling our ego trip a bit, what is lost by admitting that a creating God seems way ahead of us in knowledge ? Will this kill you to acknowledge this? Will it cause you to throw up your hands and research no longer ?
The counter question is: What's the harm in admitting you don't know that the creator is intelligent? Will it cause you to throw up you hands and worship no longer?
I have a problem with believing that Darwiniam gradualism can explain ALL that we see.
Good. It can't. Nor can Newtonian Mechanics.
But evolution gives an explanatory framework to operate within to either explain a biological feature or to develop a research program with which to do so.
And it keeps cranking out those results.
I get it though: You are incredulous that these things can be explained in these terms. Here we're talking about morals. Do you have some specific moral idea that simply cannot possibly be described in evolutionary terms?
If there are any other specific features you think evolution fails on, there are many threads and able-minded biology fans out there to help you get an answer.