The biggest advantage to the vault is it stores every version you check in, so you can revert back to an older version of a file easier. Searching capability is probably better too. The downside is that it has stricter naming conventions and higher maintenance. On top of all that it makes migration a pain and is horrible for long term storage because design reuse is a pain. Probably the biggest fundamental issue with it is library files. It makes you store redundant copies, one in the vault and one on disk. Now you are left with duplicate data, yet each data set is manipulated using a different set of rules for file naming. This is just to fundamentally flawed.
I would recommend semi-isolated. Just get used to the quirks such as:
Checkout doesn't work right when modifying properties.
When you save a part for the first time always pick the search path for the files location and not the workspace. And god forbid don't hit CANCEL CHECKOUT before you've checked it in or you file may be gone forever.
When you make changes to a piece part, then open a referencing file like an assembly it will want to be saved. When you hit save it will tell you it must be checked out. Say yes and it will fail. Just check things out from the browser first before saving.
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