1. Gear
a. There MUST NOT exist a concept as an overall Best In Slot item for ALL situations
Or at least not for all slots. Different pieces of gear should be better in different situations.
This doesn't have to be extremely extend so that each player has a ton of gear, for a ton of situations. Things must be a bit more situational then now.
This game is too young and far too little content for this to be discussed too deeply right now. There are various opinions and some different BiS setups for classes, but you have to consider that there's very little to pick from the pool at this time.

Resistance mechanics are a double edged sword. Please be careful what you wish for.

2. Cross-class abilities
There are a couple of rules here, in fact quite simple:
a. The number of really useful cross-class abilities for a certain job must be significantly HIGHER than the number of cross-class slots available
While I think it would be nice to have maybe 1 more slot, certainly not 5 more. They might as well auto-grant the abilities instead of crossing them over if you asked for this and we'd likely lose some of the abilities that can be crossed over. I respectfully disagree, sir.

b. Some traits should be cross-class, taking a cross-class slot as well
This just helps on having more useful things to choose from. Allow my PLD to get a trait from a mage that increases my MP, so that I can spam Flash if a certain fight requires me to pick up a lot of adds. Just an example...
There's too much room for abuse on this. The benefits would have to be pretty small. =.(

3. Cooperation
I really think we need jobs to interact with each other in a more interesting ways. This means there should exist mechanics that force the players to cooperate in order to reach maximum efficiency.
You're pretty much asking for FFXI's Weaponskill system. There would be +/- to this. One of the biggest things that is likely to happen is job bias, because the playerbase would want to make a "perfect" group that works well with their skills.