You can flag civilization as unplayable for you or the AI or just delete it altogether with the editor though deleting anything from the game will most likely crash the game due to foreign key constrains that the game doesn't warn you about until you run the game.
You can edit/add/delete any cultural bonus/building with the editor, but this is a rather painful process.
The gold/production upkeep can be rather crippling if you try to field an army, and what makes it worse is that there isn't even a hint that you're paying for this stuff (never saw anything about production maintenance, but it's mentioned in the XML files) or that it scales up exponentially.
Thankfully a lot of this stuff is already being worked on by the modders, so you can just take the mods that do what you want. Now if you want someone to make a Roman Bath House you might have to know someone who has a lot of time and is bored (well it's not really that hard, but unlikely people will just spontaneously decide to do that). There's a mod that eliminates the exponential scaling for gold on unit upkeep, but it only works some of the time.
I noticed people make some really overpowered civilizations, like one guy had a Celtic where all foot, mounted, and gunpowder units get double attack and that was the guy doing the tutorial for how to use the SDK. I mean I realize the point is to demonstrate what you can do with the SDK but that isn't even remotely balanced as this game greatly favors the aggressor.
Some of the changes I like (from mods) are the lowering cost of Stables (it's rare you'll ever train enough units to make up for the time it takes to build it), and take away maintenance costs on some buildings like Granary and Water Mills (upkeep on them is pretty high for the minimal benefits).
I'm not sure what's meant by an effective border defense. Obviously you can stop AI easily once inside your border if you have Oligarchy researched with just the radius around your city assuming you're not hopelessly outmatched in both technology + numbers. It remains to be seen if this is an effective defense mechanism against real players. I've been experimenting 3X culture rate, which means you'll have pretty large borders and relatively easy access to policies (just disable cultural victory, it's kind of dumb anyway). With a large amount of culture you'll have large borders, and this makes Nationalism easy to get, which means you're very vulnerable while fighting outside of your border due to the stacking bonuses and hopefully this will see more movement and tactics since I imagine you cannot wage war against a 100% combat strength deficit (from being defender to aggressor) for extended amount of time, which means the defense only need to delay people inside your border for a few turns before the reinforcements get there and force the other guy to retreat. At least, that's how I envisioned it could work out. Here's some hypothetical example, assuming you get Rifleman (25), Artillery (range 25?), Cavalry (28?) as your only units, and everything else is exactly equal and the guy with more troops will have a flanking bonus (obviously).
With Oligrachy + Nationalism the Cavalry will attack with a strength of 44.24. From my experience this will easily take out any unit the other side can field unless they've a ridiculous troops advantage, so there's no way the aggressor can fight for extended period of time. Now of course your army cannot be everywhere at once. Let's say you only have 2 Rifleman as a garrison along the border, and say you expect the enemy to have a 15% flanking bonus on you (since they have more units than you). You'll probably be fortified but you won't be attacking, so you get no bonus from nationalism, so the numbers will look like:
Your Rifleman - 25 * 1.83 = 45.75
Their Cavalry - 28 * 1.15 = 32.2
This is pretty strong odds for the defender but then your Rifleman can't be attacking either. If you tried to attack, it'd instead look like:
Rifle - 25 * 1.58 = 39.5 versus 32.2
But now on the defense, you're not fortified and you don't get Nationalism on defense, so the defense looks like:
Rifle - 25 * 1.33 = 33.25 versus 32.2
So you certainly can't just counterattack and kill the attacking army with minimal troops. You can defend pretty well but then they can just try to walk around you or bombard from range if you're not leaving your fortified positions. Also if you're really just staying fortified the whole time there's nothing stopping the enemy from attempting to completely surround you, and at that point they can definitely overpower you. However it takes a while to get a large flanking bonus due to ZOC. In theory, a good defense would stall the opponents long enough until your offensive units can get there, if you assume the other guy is smart enough to withdraw when he sees the Cavalry coming.