Turning cover into a job trait that is always active sounds way too powerful to me, so I woudn't support that. If they would make any changes to cover, i'd like to see it to where it automatically leaps in front of the person you cover like on all the other FF games. That would be nice - as trying to position yourself with that move can be a huge pain in the butt.
I like your change our defense traits into damage reduction traits though. Similiar to the change they did with Sentinel a long time ago, so that suggestion I would support.
I think our shield mastery is fine as is.
Giving Paladins a "counter" ability seems kind of weird to me. I'm not opposed to the idea of adding some kind of retaliation move - but that's a monk thing really, and I'd liek to see the jobs on this game retain their individualality.