As I've tried to explain before, the scientific establishment ("the academy" - a patently absurd attempt to demonize scientists as evil) has analyzed and rejected the arguments of intelligent design, time and time again. The problem with ID isn't that it's too damning a criticism to talk about - it's that (1) it's a criticism that's been answered before, (2) it dishonestly misrepresents the status of the scientific literature, and attempts to circumvent review by going to the public, and (3) having assumed the failures of science, it doesn't seek new scientific answers, but rather it improperly substitutes unscientific guesswork. Let's go by them, part by part.
First, evolution is not abiogenesis. Evolution considers life from first cell to modern organisms. If you and Ben Stein could get that right, we'd be in a better position.
Legitimate Criticisms of Evolution
Now, many people level legitimate criticisms at evolutionary theory. Science depends upon accepted theories getting pushback... legitimate pushback. And evolution receives more than its fair share. One of the critiques that the uninitiated level at evolutionary theory is that it's "Darwinism" - in fact, nothing could be farther from the truth. While the central precept of natural selection remains, the corpus of knowledge defining evolution has been built upon, criticized, and rebuilt countless times over the years. Professors build their careers on researching, and arguing for, gradualism versus punctuated equilibria models, so arguments "critical" of evolution frequently grace the pages of peer reviewed journals. People like PZ Myers are involved on a daily basis in reinventing the theory. To say it's intellectually dead is simply ignorant. In fact, researchers often challenge whether or not evolution can account for Organism X, or Trait Y, or Appendage Z. Of course, when someone comes up with an example of something that can't be, at the moment, explained by evolution, the first thing that they do isn't throw up their hands and declare evolution dead! Science depends upon the accumulation of knowledge towards a common, mutual understanding - so they do more research. Thomas Kuhn, in his Structure of Scientific Revolutions (which is really a must-read for an anti-science type like yourself), explained best that this is the way that science works. A general theory exists, and scientists poke & fill holes in the theory on a daily basis. Over time, real holes emerge, that can't be accounted for by the current theory. Eventually, the holes overwhelm the theory, and a great mind comes up with a new theory to account for the previously unexplainable.
The Structure of Scientific Revolutions & the Flagellum
Now, let's picture the modern synthesis of any theory as a dam. And, imagine the "problems" faced by the theory, or issues that it can't explain, as water building up behind the dam. Kuhn hypothesizes that "the structure of scientific revolutions" is that the water builds up to a critical point, until it spills over. Intelligent design posits that the dam has burst. However, the "water" that ID creationists think breaks the dam has, in fact, been "drained" for quite a while! Which is to say, the "problems" that ID creationists imagine exist, are no problems at all.
The flagellum is a common example. ID creationists continually say, "this can't have been generated by a gradual process" - on the contrary... it's been explained for a good long while, too. One of my socks gave you a good link to follow to learn about it. It's pretty high level stuff, so you might need to learn more about biology before you'd feel comfortable reading it. But the end result is that the flagellum fits squarely within the evolutionary paradigm. The "water" has long since been drained.
The Flagellum Proves Evolution
Further, cases like the flagellum actually supplement evolutionary theory. One of the requirements for an explanation of the physical world to qualify as science, is that it must generate testable and falsifiable predictions. Now, according to evolution, many species diverged at their early history, and independently evolved. However, the fascinating thing is that a good deal of species that are around today look alike, and use similar organs and body structures. If they evolved separately - rather than being created or designed - evolution would hypothesize that these similar structures may serve the same function, but if the species have a different history, probably had different intermediate forms, and therefore a different terminal makeup. Put in other terms, they should do the same thing, but do it differently, since their intermediate forms were different. In fact, this prediction of evolution is time and again borne out by the evidence. While many species and forms of life have flagella, different species have flagella that work in different ways. Their makeup is unique, if their end result is the same. This is "convergent evolution" - another prediction of evolutionary theory that is borne out in the process of giving the lie to irreducible complexity. Not only does the case of the flagellum drain the water from behind the dam, it makes the dam stronger!
ID Appeals to the Public, but Not to Science
ID creationists don't meet these arguments at all. Rather than trying to redo the research, or examine the research in detail, they either evade the proof or claim it doesn't exist, creating a "manufactured controversy," or "manufactroversy," where ID poses a problem, scientists answer it, and the ID creationists close their ears to the proferred explanation on ideological grounds. Granted, some ID creationists abandon their theories altogether - look at Behe. He's come a long way from Darwin's Black Box, and now has actually abandoned his previous theory about the flagella!
To get around the issue of proving to the scientific community the "problem" with evolution - since science has already solved the problem - ID tries to put the case to the public, exploiting the public's poor understanding of science, and arguments from awe, to gain popular credibility at the expense of legitimate argumentation. More than anything else, this gives the lie to the notion that ID is scientific - as Kuhn, and many other scientists have said, science doesn't answer to political consensus.
Further, let's assume that the flagellum seemed an unresolved evolutionary issue. The proper answer to that - the scientific answer - isn't to declare "victory over evolution" (which is what ID creationists do, proving themselves again to be issue advocates, not scientists!), but is rather to do more research to ascertain the nature of the problem, and solve it. This is to say, the imaginary flagellum problem could be water behind the dam, but it probably wouldn't break the dam. Alternately, if the flagellum was a real problem, ID creationists could come up with a real theory.
Your reply, undoubtedly, will be that intelligent design is a scientific theory. Of course, it's not. Science is defined as the materialistic study of the world. You may object that this excludes religion, but if it does, it does so properly. Think of the goals that science serves. Arguably, the world is part material and part spiritual. The material world, we know, has certain rules that control its motions, like gravity, the curve of relativistic spacetime, and mathematics. It can be understood, and often manipulated.
Science seeks to move towards establishing an objective understanding of the world, from which all (regardless of religion or language) can learn. Alternately, science seeks to descry the objective nature of the world, to allow its understanding and manipulation by mankind towards more a more favorable world (through engineering). Only materialism is adequate to that task - the rules discovered by science have to be objective and baseline to be useful to all, and to be applicable to fabricating solutions to problems faced by humanity. For example, a religious explanation of the origin of human life may be nice to think about, and it may be comforting. But it doesn't allow the solution of real-world problems - such as understanding and eradicating evolving bacteria - because it doesn't go to the fundamental, mathematical, mechanistic nature of the universe. It goes to a personal understanding.
So, science is great. And it works. You're still alive, aren't you, after I presume a couple bouts with sickness? So if we're to abandon the laudable goal of attempting to understand the universe and manipulate it, there had better be a damn good reason - for one, science had better not be up to the task. To abandon scientific explanations of an issue would be to not only abandon the paradigm operated within by scientists, but it would be to abandon an entire line of human inquiry. So, the problem faced by science should be proportional to the drastic action taken. Science has yet to encounter, in evolutionary biology, an objective limit that suggests the fundamental un-understand-ability of evolution... and if you're hoping for a science-stopper, the flagellum isn't it.
Intelligent Design Violates the Scientific Method - Reason 1 of 1,033,100
By appealing to the supernatural, then, intelligent design creationism abandons the materialistic basis of science, and abandons the unique benefits that the scientific process alone can secure. If science is to have any meaning at all, intelligent design is not science.
All of this is to say that the materialistic basis of science, the fundamental gift of the enlightenment to humanity, has serious benefits, and ought to be pursued wherever possible. Intelligent design is a theory outside this paradigm. While some situations may justify stepping outside the materialistic paradigm, the imaginary, asked-and-answered problem of the flagellum et al doesn't make evolution one of those instances.
And that's why scientists dismiss intelligent design.
Now, this poses a couple problems for you. If you can't answer these problems... maybe you shouldn't be trying to force others to buy into your poorly-thought out worldview.