1. Several Duchies. This has always stuck out as a weird thing for me. You can be the ruler of the known world, stretching from Britannia to India, but my god do your vassals hate you for being in charge of THREE duchies instead of TWO. How DARE you?! Preposterous!
A solution here is to tie the minimum Duchy limit either to your personal ruler tier (Duke, King, Emperor), or the realm holding size. It is hard to communicate to the player a realm size limit to it, without getting into numbers etc, so it is probably easier to directly connect it into ruler tier. You are a Duke? 2 Duchies without any opinion maluses. King? 3 Duchies, etc. It's a natural progression, and it makes sense as you progress through the game.
I would favour integrating it into the demesne limit, as some have suggested it. Seem more coherent to me: I prefers that few game concepts would cover much each, rather than much game concept covering few each...
If we want to avoid getting into numbers, we can considerate that the demesne limit is a limitation of landed titles and that any title, being baron ranked, count ranked, duke ranked, king ranked or emperor ranked, count for one. So to have three duchies instead of two while staying under the demesne limit, you'll have to renounce to one barony.
A more subtle solution would be to have baron titles counting as one holding and duchy titles counting as two holdings, or whatever the good balance is decided to be.
Then you let players cook with their demesne limit as they wish... It is, in my humble opinion, the funnier. Player can held a third duchy without penalty if they renounce to two baronies (if one barony count for half a duchy)... And if they only hold one duchy, they can hold two baronies more than if they held two duchies...
2. Titular Titles. Titular titles have always sort of annoyed me. They are meaningless titles you can use specifically to gain prestige or make Merchant Republics, and that's all they do. I am going to make a change here, coming out with the next expansion, where you can no longer create titular titles by simply holding their capital city. They will all be changed into decisions instead, and when you use the decision and form the Kingdom title, you have a certain amount of DeJure land drifted into the title. Good examples of this currently in the game are the Spanish kingdoms. You use the decision to form Aragon, and the Duchy of Aragon and Barcelona are drifted into the Kingdom title. So if the title are a titular one, you should have a decision to form it, if it has land attached to it, you simply hold enough land to create it. Hopefully that will reduce the Kingdom tier spam somewhat, in the late game.
Is it needed to rely on decisions? Wouldn't it be possible to do it trough the gain_effect and allow brackets on the titular title definition? It would be more cleaner in my humble opinion.
Anyway, while I do not like titular titles, for similar reasons as yours', I quite not like your potential solution as it will tend to make this game even more easy than it is and because I find it incoherent. Why would such a title gain immediately and magically a legitimate territory while another one would have to wait one century? It seem too much gamey.
My advice is that there is three case of landed titles:
1. titles of the past (before the game start, before the current moment of the game),
2. titles of the present (at the game start, at the current moment of the game) and
3. titles of the future (scripted while didn't happened yet at game start nor at the current moment of the game).
In my humble opinion, titles of a (relative) past and titles of present perfectly fit the
de jure system. However titles of the future shouldn't be present, neither as
de jure titles (I don't want to have a de jure Russian empire in 769!) nor as titular titles. Since Charlemagne, Crusader Kings is able to rely on dynamic titles. It would be quite more interesting to use it, with two kinds of conditions: very difficult conditions to meet if created somewhere there is already a similarly ranked de jure title, quite more easier if created somewhere there is no de jure titles.
It would be difficult for a Frank lord to found royal legitimacy in the Gauls without referring to Aquitaine, Burgundy, Provence, Brittanny, Neustria, Austrasia, East France who weight much on the royal symbolic of his place... However, it would be quite easier for a Varegue to found royal legitimacy in territories that never new any organized and stable kingdom before: he is in a quasi
tabula rasa place.
If created in a territory which was once
de jure part of a titular title with a title history and with similar religion, then we might imagine that, instead of creating a new dynamic title, the creation decision would instead recreate again the title...
3. Multiple Empires. Now this is the one I have a hard time coming up with a good solution to. I don't feel like there is any simple good solution to this problem, as things stand right now. One idea I was playing around with, is to incorporate empires into your original one. Either by outright saying "Hey, you are in charge of the whole DeJure area of both Italia and the Roman Empire, so we'll give you a decision to incorporate the Empire of Italia into your other DeJure lands."
Another solution could be to halfway incorporate two titles into one title, and say "Empire of Italia and Germania", share the DeJure lands, but have different succession laws so the two titles could fall apart if you had different heirs. This solution is code heavy though, and will probably lead to a lot of weird bugs, as well as horrendous bordergore and weird vassal splitting.
The final solution is simply removing the opinion malus on having several empire titles. I don't really have any data saying this is good or bad.
The second solution is the best one: it is coherent with the universal ideology of an empire while allowing empire to split anyway (considering that their
de jure lands would split again too), but as you say that it is code heavy, the last solution is the one I would prefer over the first one: Magically integrating new empires into the original one is waaaaay top gamey for my taste. Merging two titles in one have few interest and lose the opportunity to have two empires with distinct successions laws, distinct crown laws. It would impoverish the game rather than enriching it.