On the issue of Protect:

1.0 players will remember that protect used to be similar to what a lot of people here are suggesting. It was a buff that lasted only a few minutes at most, just long enough for one fight or so at the time. When Yoshi-P took over he expressed dislike and it was one of the first spells he changed. He wanted to remove it completely but was concerned of the iconic status it holds.

On the issue of cross class skills:

What the OP proposes is more like a cross class synergy system rather than a cross class skill system. The OPs idea basically encourages players to level all jobs not just the ones you can cross class skills for. Another example would be "level all disciple of magic and you get a bonus 30 INT or MND across the board". Therefore it is already a better system than the one in place. It also reminds me somewhat of 1.0's cross class "guild token" system.

Sadly I see an overhaul bringing things back to basics and being really unsatisfying. I would have loved SE to go 10 steps further and actually made a full on Junctioning system for passives and cross classes where abilities/traits can be modified completely like from single target to aoe, to en-element damage, etc. Sadly I never see that. We have to have a limited system otherwise SE will not be able to churn out content fast enough (easier to balance etc)