Im not sure why you would continue attacking an enemy which you're clearly not strong enough to take out. If they're in their own borders, they're gonna heal and if you aren't doing enough damage then you're not going to take them out. Of course they'll gain XP, they're engaged in battle. Maybe its a little lame that they're just sitting there, but they still deserve something for surviving battle. Besides, wasn't your Trireme levelling as well?
The Militaristic CS asked you for a favor and you did it. That makes them your Ally until it degrades. They will occasionally gift you units, and you can ask them to stop whenever you want. I personally haven't seen the rate so extreme that it would be considered an exploit. The production rate is probably on par or slower than what you could produce yourself, but that is entirely circumstantial
I'm not sure what the complaint is here. If you don't want to do a quest, then don't do it? Are you mad that they included extra things to do in the game?
There are trade-offs to settling a new city. Culture costs rise. Happiness decreases. Maintenance costs rise. Sure, city sprawl is a simple, effective and often used tactic, but I wouldn't consider popping cities up everywhere just to fight a unit. The costs and effectiveness of a simple combat unit that can move and fight are a much better tradeoff. Also, there's tension trying to run a settler through hostile lands. If an enemy even touches your settler, they're gone unless you fight back for them.
There are no buildings that are +1 food. The granary gives +2 food for -1 gold maintenance. The Lighthouse gives +1 food PER water tile worked. I will admit though, I rarely find the granary worth it and only build lighthouses if I find my coastal cities are stagnating.
You can move onto an embarked unit and instantly destroy it, if it is unable to defend itself (Askia's embarked units can defend), which I guess you could consider like a ramming ability.
I haven't played many previous Civilization titles, so I'm not sure if hit-and-run was ever available. From a RISK and other world-conquering strategy game standpoint, it's pretty common that you can't move after an attack. You're fatigued from battle. It would be cheap to be able to run in, attack someone, then run away repeatedly.
That should not be true. Combat units can stack with non-combat units at any time. 1UPT really means 1 non-combat + 1 combat UPT.
Not sure what to say here really. Early game cities are a little on the weak side, but I've definitely lost quite a few units trying to attack cities. Maybe you're just playing on too low of a difficulty?
I don't know anything about cottages, but there are still tile improvements and most military units can pillage an improvement (farm, mine, etc). If a city was already depending on that improvement for gold or food, you've just cost them that income.
Sorry, but overall you sound like you're just nitpicking and wishing this was just another Civ 4 expansion. From what I can tell, its a different game. That doesn't make it boring or bad, for me at least.