I've either been amazed about the abilities of Agisoft to align photo's and been frustrated about it's unabilities....when I can I shoot concentric circles around the object, either using the turntable method or not....depending on the object's size. I've noticed that overlap is important but Agisoft has had some problems with:
1) Chunks.....individually alligned chunks did not have the same scale meaning reshoot please...this could be my error hard to tell, and personally I'm solution oriented in my work approach, meaning that I don't linger on checking the why but focus on prevention in the future....I standardised my shooting approach as much as possible (see above).
2) Infil shots.....when you have a complex model (lets say a Matchbox Model truck) I like to take infil shots to pay extra attention on certain sight lines I would be missing in the concentric circles, well this seems to baffle Agisoft sometimes. So I stopped bothering with these....Agisoft has it's own logic for filling in holes, and it means that even with smal details caught (and masked out) I can still be confronted with some unwanted action form Agisoft.
3) Mask. I always mask, you means always, like in always? Yes.....always. I know it sucks and it's feels like real work, but it improves allignment and improves scans. Especially white sky, blue sky and trees in front of buildings, waving trees are the arch enemy of any Agisoft scanner. So mask them out and shoot around them.....it will improve alignment. If can get behind them, if not well you're gonna end up with a partially wavy scan or a scan with some ugly holes.
4) Depth of field....aperture 22 is minimum for shooting macro (and a APS-H or C sensor is preferred over a FF) since DOF is bigger.
5) Don't use flash....unless you know what your doing. I use a ringflash (idea of a german paleontologist and those people are never wrong about anything :-)). Keep the ligth as even a possible, use a tripod and if needed one ore two fill in flashes just to white out the background. Then Magic Wand selection in masking is a breeze....
Does this get 100% predictable results, no. there are still nasty and wonderfull supprises. Like thos bottle opener....tried it with laser, no scan, tried it using SLS no allignment between back and front. With Agisoft first time right.
Greets, Ed.