Just a thought on the Roman faction for your second invasion - particularly if you're worried about the human player having total control before the Romans show up you could go for an 'invited invasion' approach, whereby under certain conditions the Romans would step in to aid a friendly tribe. It's not entirely infeasible and might even have been more likely than a full scale unwelcome challenge.
You could build in something so that once one player gets over X territories then one or more of the other factions gets an option to do a deal with the Romans to get them involved, initially against the strongest faction but if they get a foothold then against everyone who might oppose them. You could even let it start off by just allowing recruitment of some Roman units (in ports?) for the factions requesting Roman aid but with a count-down to full invasion.
Alternatively you could build in some culture/religion effect and have that as a trigger, e.g. trading relations with Rome can be established giving a large boost to income but storing up invasion shaped problems for later.
Feel free to ignore these ideas liberally by the way - my own half attempt at a mod has fairly much drowned under the weight of semi-ideas I've thrown at it...
How developed are your druid/pope plans? Sticking with the same idea you could have the 'excommunication' equivalent being relatively hard to come by but be effectively lead, if the other conditions are right, to something quite against the 'tallest poppy'. The campaign ai can be set to be quite aggressive against someone over X territories too / friendly to other opponents of that person so it might not be needed to use the druids too much for that.
Possibly lastly, following from some of the more recent TW series games, could you try and implement some different scale settlements, so one regional hub (be it hillfort or town (city/castle?)) with several minor villages around. If possible then some penalty for the owners of those villages if the central settlement isn't owned could be interesting.
I think that's it for my daft ideas for now. Good luck with the mod