I also like that Preview gets page numbers right in complex documents like textbooks. If a problem set is on page 89 (which might be the 115th actual page), I can just go to it. I’ve yet to see any other free or built in PDF reader do that.
I do agree that the annotation feature isn't like Omnigraffle or draw.io diagramming apps that are based around a mouse; the interface does seem more suitable for a touch (pad, screen). You choose an object to add, then get to move it into place rather than selecting an object to add and then use the mouse to place and size it. The annotation feature also works in a very similar way on an iPad / iPhone.
If you tap (click) and /hold/ anywhere in the hit zone of an object the cursor will move to a hand and you can move it anywhere. For a text box, the hit zone it is almost anywhere on the text - yup, it is more awkward if you delete all the text! The resize / reshape hit zones for objects are centered around the "dots" when the object is active. A single tap (click) will edit text.
I am not sure what is happening when things disappear and cmd-Z doesn't undo, I've not experienced that.
This markup feature is also available when annotating image attachments in email.
It would be nice to be able to group more than a single set of objects and keep them grouped.
I've used the annotation feature quite a lot to highlight errors in web pages and give sequence instructions on how to do something on a poorly designed site.
Be careful of PDF's with built in broken fields though, in which case I just add a text field on top if it's easier.
There should be nothing "wrong" I can do which makes text disappear which can't be undone, or where the click-and-drag targets are as tiny as can be.
The program is buggy. Apple releases bad software sometimes. That is simply all there is to it.
You said "mouse", is it a gaming mouse? Is it configured to issue a bazillion clicks if you press and hold "left" button - for a stupidly small number of ms, taking no consideration of you if you are playing a game? Does it also send "wiggler" (WASD) keyboard presses at the same time? Either of these will ruin any chance of you doing "undo", unless you also "undo" a bazillion times. This behavior will likely make a lot of other things behave in quite weird ways and be "slow" to respond. If you've got a gaming mouse doing auto-clicks, auto-kbd strokes for non-game apps, then the UI designed for humans is going to behave weirdly.
FWIW, the placeholder text can never really disappear, if you remove it all, you get the placeholder "Text" back again. You can replace it with a single space, but that also has a hit zone of more than 1px both H & V. Maybe you have found a bug. I do think there are issues with font background / foreground colour selection that might make it "invisible", but the hit zone will still be there.
I use an ancient mouse, "Microsoft Comfort Optical Mouse 1000" and an Apple Trackpad. I cannot reproduce what you describe.
What mouse are you using? What additional HID (Mouse, KBD) extensions do you have installed?
And, no. This is 100% Apple hardware and software. I am using Apple's trackpad, built into one of the most recent Apple laptops, using the latest Apple desktop OS.
Semi new thing is the removal of proper "save as" in Preview and other 1P apps starting in Lion. Still sucks and still hasn't caught on in 3P apps.
And no tooltips either. Even by clicking I couldn't figure out what most of the buttons even do. A lot of them seem to do absolutely nothing. The only thing I've learned is to summon a randomly sized box on a random position and then struggle to resize and reposition it.