One big disadvantage to using a transparent proxy is that you're unable to force users to authenticate prior to gaining access without resorting to something more complex like a captive portal:
You then risk breaking lots of tools that have no problem running properly configured with a regular proxy, and force your users to actually use a browser even if their work does not require one.
In a related vein, it's also more difficult to use ACLs per-user or per-group.
If you're not interested in authenticating your users or using ACLs then you might be better off with a transparent proxy because of its ease of deploying (basically no configuration needed on the client), of course.
Transparent proxies are also less good at handling https - the two options are to use SNI (which requires a recent browser) which will give accurate domain information, which can be used for monitoring, blocking or kicking off some sort of MITM, and reverse-dns which is possibly accurate enough for monitoring and not much else.
One big disadvantage to using a transparent proxy is that you're unable to force users to authenticate prior to gaining access without resorting to something more complex like a captive portal:
http://en.wikipedia.org/wiki/Captive_portal
You then risk breaking lots of tools that have no problem running properly configured with a regular proxy, and force your users to actually use a browser even if their work does not require one.
In a related vein, it's also more difficult to use ACLs per-user or per-group.
If you're not interested in authenticating your users or using ACLs then you might be better off with a transparent proxy because of its ease of deploying (basically no configuration needed on the client), of course.
Transparent proxies are also less good at handling https - the two options are to use SNI (which requires a recent browser) which will give accurate domain information, which can be used for monitoring, blocking or kicking off some sort of MITM, and reverse-dns which is possibly accurate enough for monitoring and not much else.
Another one is that you can not bypass them. If your proxy is stuck or soemthing, the user can not just try to load a site without.