First of all, a little background, I've been playing Total War games for about 12 years now starting with Rome 1. As your titles have increased in magnitude and depth, I find myself more and more invested in your line as opposed to the yahoos in Sweden who can't seem to keep their trains on the rails.
So, I want to discuss two areas I feel Rome 2 is lacking in: Diplomacy, and the consequences of war.
So, diplomacy to build relations works pretty well for the current "level" of depth: You have non-aggression pacts to establish cordial relations, trade agreements to boost resources and income (though I wish this was a bit more custom as to what's being traded, military access, defensive pacts, and full alliances ready to kick butt and take names. Where it lacks is in the deterioration of relations; the only way to really get at an opponent is to declare war, or grant military access to a current foe of theirs (though this is very circumstantial in application). Sure you can deploy agents to sabotage their armies and locales, but that entire system feels outdated and tedious, to have to recruit these agents and click them around the map every turn for the sake of their functionality. The whole system needs to go the way of the Diplomat and be integrated into the Diplomacy UI, or even a separate one for 'Intrigue'. The functionality wouldn't really need to change; from an overhead map view you could select provinces or armies, attempt to disrupt them with timed effects calculated by distance, and should the action fail, your faction suffers a penalty likely tied to the difficulty of future intrigue against said army or city.
Secondly, war is typically of no consequence in Rome 2. Now as a disclaimer, I appreciate this it Total War: Rome 2 and not Europa Universalis: Rome, that largely being able to just march across a border and conquer to one's content is a core component of the experience. Still, there's things that can be done to take away the arcade-y feel:
-Abstract Population/Recruiting Pools: Simply abstract Civ-style number generated from the number of settlements and their size. It would make players be more considerate of wantonly declaring war and how long to pursue it. The system could be expanded on to add penalties for depleting the pool and bonuses for it staying (mostly) full. I would like to note a depleted recruiting pool was the primary reason Gaius Marius bothered to reform the Roman military into the (mostly) unstoppable legions we all think of.
-Supply Lines: This is already represented by attrition and food, but it could be a lot clearer as to where your supplies are coming from. It's confusing when I see I'm in -5 food because the Etruscans just revolted in Velathri and my Rome garrison is starving, but I go and check my army in Iberia and it's well-fed and toasty because... reasons.
-Sacking Settlements: A scorched earth strategy should be a thing, but it's incredibly foolish to raze any settlement in Rome 2 because unlike in Attila, you have to keep the settlements. Why do I want to tear it down to the foundations and lose all the food and income generation and other bonuses? Why can't I just wreck it and leave?
Just some suggestions and food for thought. I hope others add and this can become a great feedback thread, and I hope the developers see this not as off-put criticism, but friendly critique. You guys are making headway, and we want you to be able to fire on all 8 cylinders and net both the hardcore Grand Strategy players and the jocks that saw their brainy little brothers playing it.