One thing that sucks is, as I said, you get no advantage for having an enclosed resource other than your city has to be attacked for the enemy to destroy that improvement.
But let's be realistic.
A) There's no resource that valuable that you'd want or need to go through a whole city just to get to it. Destroying or capturing a city would also be more valuable in the first place. Because obviously you're not going to claim that resource from the enemy without dealing with the city first.
A1) Destroying a single resource, or even a handful, has no real effect on the enemy at this stage of the game. Their economies are broken, they build cities like crazy, and unless the AI is failing terribly, you're not going to make a dent.
So far it seems like the exception rather than the rule that an enemy gets within your territory. With the travel spells, there's really no excuse for letting them rampage around destroying your outlying improvements. It's not that hard to defend your turf, so there's less benefit to enclosing, even when you're sandwiched between two hostile empires.
Along with that, what's resulting in a lot of confusion is....
Yeah, depending on need, I try to daisy chain resources with improvements as much as possible and limit how many improvements I use purely for their bonuses. Especially if you already have a Lost Library or two (or whatever), building a study isn't doing you much unless you have -a lot- of them. You'd need 5 cities with a bunch of bonuses to equal 1 LL with a handful of bonuses.
This. Sure it says Research +25%, Research +100%, but those numbers don't translate very well. If LL produced 5, and a Study produces one, people would go "Oh, I don't need a library or any of this other crap!" Or at least they would see the tile vs. resource value trade off a lot more clearly. As it is, with your average city, you can build things all the way up to Level 3 and not miss anything, But levels 4 and 5 are where you run into the tile cap, by which point your city is already big and nuking it requires tediously going tile-by-tile to find what needs to go.
So I really think resources enclosed within your city need to provide an additional advantage over being defended.