Easier to transfer (reworded from "less files to transfer")
A zip file is one file. Is it really more files to transfer. Assuming package works properly its the right thing to do.
But obviously this is simpler if you don't consider your workflow that important. Which is a boon to casual users.
Not really a pro or con really, just a social issue.
No broken links
Here however is have to say that technical people deal with these kinds of things all the time. So even if inDesign does not allways succed in packaging there should be no reason why it would be a big deal to handle packaging yourself.
I mean i have lots of game/media programming projects that have files in the 10,000's (mostly sound, video and sprite assets) and have never had any problems with ensuring all files are moved correctly between computers (and less work and file overhead than using something like zip files). There are good solutions that are magnitudes more robust than what inDesign gives you. They will even handle the transfer of files over to your client without any extra effort on your part.
Heavier InDesign file
Not only that, but you now have same file on disk multiple times for every version you save. The files logical connection with any workflow is broken and can no longer be updated in isolation or by third parties. It makes it harder for several people to work on separate elements simultaneously.
This may mean that a simple update is now changing 20 things in several separate files. So you need to weigh in if the benefits over the costs of checking and rechecking. It is also a burden to your backing up and versioning of files. But then on the other hand now you are isolated form mistakes in change management (did you consider that all these files were affected?). A bit of a mixed issue not really a pro or con.
SO this may be a Pro or a Con depending on your workflow. Though you can also do this kind if insulation with separate files too. But this is really just a symptom of inadequate version control. Which admittedly is typical to graphic designers because there is not many industry specific solutions for this and thus many haven't heard of such things.
Cannot see all the information in the links panel (resolution, etc.) without dis-embedding
Yeah that's just stupid design on Adobes part. You could easily fix this for your workflow with a scripted panel. Quite minor thing
If one image is corrupt, may corrupt the whole InDesign file
Again a symptom of inadequate version control. But yeah likelyhood of file corruption ofcourse increases with file size.