I'll reply to specifics, below:
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1. Witness has a greater number of finishes and also has the choice of wooden or rubber grips. The 97B has two types of finishes, and only wooden grips are available
Important only if you really want a finish or grip not available with the CZ. Doesn't make the Witness "better," per se.
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2. Magazines fit flush into the Witness, while the 97B has a 2-1/2mm gap.
Nice characteristic. The new CZs come with a different base plate that fills the gap.
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3. The dots on the sights of the Witness are carefully applied, forming 3 perfect circles. On every CZ pistol I've handled (including the P0-1 and 97B), the dots were smeared and injected poorly.
That has definitely NOT been my experience, and I've had eight different CZs.
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4. Straighter and more precise machining on the Witness.
Again, that has not been my experience. In fact, my CZ-97B (traded away), was one of the most nicely finished guns I've bought in the last several years.
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5. 97B has an un-necessary barrel bushing which decreases accuracy if somewhat loose.
Perhaps, perhaps not. Let your Witness get a little worn around the front of the slide and see what happens to accuracy. With the CZ, you just order a new bushing. (A loose bushing, incidentally, shouldn't greatly affect accuracy, unless its so loose as to allow wobble.)
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6. Full length metal guide rod on the Witness. Half length plastic on the 97B.
So? Explain how a full length guide rod is BETTER? (This is a long-running debate here on the forum.)
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7. Two barrel brushes included for the Witness as apposed to one for the 97B.
Do you actually use the factory-supplied brushes for anything?!
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8. Better price for the Witness.
Less expensive, but it could be argued that you don't get as much.
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9. CZ replacement parts are overpriced, and the customer support REALLY stinks. I don't know about EAA however, could be the same story.
Parts are expensive. But my experience with customer support (and that of most people I've talked with) puts CZ-USA right up there with Ruger and Kel-Tec as being one of the best in the business. Witness (EAA) has long been one of the horror stories of the gun industry and one of the reasons given for NOT BUYING A WITNESS or CZ Clone. They seem to be getting better.
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So the question is, why buy a 97B over a Witness .45?
Few of the reasons you cite are meaningful. Only "PRICE" of those cited above seems meaningful, to me. And I'll agree with that one.
Some you didn't mention:
10. EAA Witnesses have a full range of conversion kits for the large-frame model, allowing you to change calibre.
11. EAA Witness large-frame guns have a smaller grip so that if the CZ-97B is too large for your hand, you have a CZ-style alternative that might be easier to shoot.
12. Much better selection of after-market parts and supplies.
13. Simpler design. (Its not really a clone; just loosely based on the CZ design.
I have an EAA Witness .45. Its one of the pricier of the Witness models -- a Sport Long Slide. I prefer it to the CZ-97B, but only because it fits my hand better. The CZ-97B trigger was much, much better than mine. (I spent MONTHS getting the Witness trigger right.) After much effort, the Witness is not a superb weapon. But it was not noticeably more accurate than the CZ-97B; wasn't less accurate either. They were both very accurate (when I did what I was supposed to do.)
Witness/Tanfoglio makes a good gun. If they get their customer service act together and improve their triggers -- which, in my experience, aren't that great (but improvable) -- they'd be hard to beat.
I have only limited experience with Baby Eagles, but they seem to be at least as good as CZs...