Why do the Ikko Ikki behave exactly like the other clans in Shogun 2? They were not so much a clan as a loosely aligned group of peasants and low nobility which admittedly I have no idea how the game would portray properly but it could have been really interesting.
To put it bluntly, Video Game Historical Revisionism. In finer terms, why go through all that trouble to "portray properly" in gameplay terms when they don't exactly get love from fellow clans and typically get wiped out quickly? They already get unique units, including special priests and a lack of metsuke. Throwing an overhauled government system on top of all that would be very frustrating and possibly too much for some players.
This period of history is subjected to a lot of Common Knowledge. The Ikko Ikki really weren't all that different in terms of how they operated, equipped, or organized then most small clans. English translations also really like to label nobles as "Samurai" even though, at that time point, "Samurai" wasn't a very well defined term. A lot of the "Peasant" vs "Samurai" vs "Ninja" conflicts were typically against two factions that functioned very similarly and got relabeled a few hundred years later to fit into these class roles.
Why is the AI so terrible with diplomacy in this series (at least in Rome and Medieval 2)? Half the time they're making either ridiculous demands or stupidly obvious bluffs. "Pay us an obscene amount of money or we will continue this war that we are clearly hilariously losing." Is this a case of poor programming or am I missing something?
Ego? In-universe, it could be explained as their having bad intelligence and thinking that the units you have bulldozing over their territories is all you have, period. At least in Medieval 2 there's the little widget on the bottom of your proposal (or counter-proposal) that mentions whether the offer is demanding or not.
It's an issue with the programming. Diplomacy and military AI do not "communicate" in the game. The diplomatic AI will look solely at factors like the ones on the diplomacy screen (relative power, reputation, current relations, money, etc), while military AI will look at the actual strategic map. The diplomacy AI literally cannot "see" the strategic map and see how badly it's getting trounced. This is also why the military AI will out-of-the-blue betray you even if you're allied; all it sees is "City with only one unit in the garrison, ATTACK NOW!" and doesn't even look at whether or not its an ally or neutral city.
In Empire, how come when Ireland have successful rebellion and gain independence from Britain, the country will be an absolute monarchy instead of a republic?
Because Irish revolutionaries weren't predominantly republican until later in history?
Also in Empire, seeing as how nationalism and independence movement play an important part in the game, why is all of modern day Spain consist of a single unify territory, instead of having Catalonia and the Basque Country as separate territories? (This is not meant to be a Flame Bait, but considering that it is possible for Scotland, Ireland, Quebec, Columbia, the United States, etc to gain independence from their home country as emergent factions, it just seems odd.)