1) Is somewhat handled by expanding influence borders, which you can improve with research/city structures. The other obvious method is stationing sentries equipped with sight enhancing gear around your kingdom.
Yeah, I suppose I could station sentries around... that seems a little wasteful but I guess it's the same deal as constructing towers. Still, a high-level enchantment that creates some sort of internal magical sensors within your borders would be pretty nice.
2) This isn't something you'll run into often, but it is an annoying bug. Should be easily fixable, just need to make resources not count against a city's tile limit
Yes, this would be the fix to the bug. I'm playing a game right now where new resources popped up adjacent to my capital as the game progressed, and got absorbed into the city's borders without my consent. The result is that the city is stunted because I can't even add more housing, let alone any of the level 4 or 5 improvements. I tried the workaround of demolishing improvements to rebuild them away from the resources (which has worked before), but every single improvement gave me the error that I couldn't demolish it because it would make my city non-contiguous. Even the improvements on the edge that clearly would leave things contiguous!
But as the game matures and more improvements are added (Town Portals, please!!), they'll have to increase the hard cap of 50 somehow. Seems like making that a researchable tech would be a good approach.
3) A high level research in the Adventure tree does create new shards on the map - I can't remember if it's Kingdom/Empire specific or if both get it though.
I think it's just a one-shot deal, though. To my knowledge, the only long-term tech in Adventure is "Refined Charm", which lowers recruitment costs for heroes and thus is totally useless. Adding another tech that continues to reveal new crystals/resources/treasures would be great. Also, making charm affect maintenance costs for units would be awesome as well.