Expanding resource spawns to the entire map is on the to-do list, as is expanding the usable game space itself.
More animals will come in the future; at the moment, the animals are placeholders and are gameplay prototypes. This is a content request, and basically it's lower priority at this stage.
Explosive Charges (C4) and Raiding
You can play on servers that have plugins to make C4 recipes and drops limited or blocked altogether. At the moment, the explosives in-game aren't particularly meant for the long-term, to the best of my knowledge, but I'm not a dev so it's not up to me. Expect an overhaul (and likely a major increase in cost, if not a decrease in power) of explosives in the future, but I have no idea when. Could be months down the road.
-more base defense options-
On the to-do.
I'm going to remind you that you're in an alpha, and this is the phase where we really want to find out how the engine breaks when tested against varying scenarios. Putting artificial constraints at this point seems to be a way of masking bugs from detection for later discovery when the limits try to get raised. I presume there will be some significant adjustment to the building limit in the future. Again, not a dev, not my call, just speculating.
You are complaining about placeholder content. This'll all change and things will make more sense as the framework of the game gets built up around it.
Take a guess what I'm gonna say here. Starts with P, ends with 'ontent'. Also, it's worth mentioning that another facet about the current phase of development, and you've probably discovered this even if you thought it was a feature, is that Rust is essentially unfair and unbalanced. Certain adjustments have been made lately to make it less unbalanced, but it still is, so radtowns kind of being lame is a bit of a lower priority until the devs want to improve a gameplay element that directly touches on or is impacted by the radtowns.
Random Computer Generated Structures in Rural Areas
Now, this is one I haven't heard before, and also happens to be one I can get behind. Prior to procedural map generation being a goal of the devs, I would've disagreed with you, but now I would be okay with little shacks and ruined homesteads generating randomly across the full-size map, once we get to play on it with uniform resource spawning. Perhaps they spawn with a reduced, but active, decay rate, so they begin to melt away promptly if not discovered and claimed as a base.
This means that, if an admin starts a new server with a random-generated terrain, and everyone hangs around an area about the size of the current Rust map's resource zone, after the first week or so, as people start making treks deeper out into the wilderness, they'll come across inexplicable ruins that simply have nothing (because the crates already decayed away or w/e) except a couple foundations and a partially-intact two-floor 1x2 chunk of building left up. In addition to the occasional time when they'll find a ruin that actually has something in these partially-decayed places, and the fresh shacks that may spawn around them with loot, this will add to the collapsing-world atmosphere, with decaying shacks that nobody but the game's random structure generator built giving a sense of an apocalyptic depopulation.
I like this one. I can't say that I fully agree with you on the exact details of what these ruins should be and what they contain and what should make them special, but that's a semantic difference. I made a thread about dynamic forest cover that fluctuates in response to harvesting activity and intensity, and I think taking that idea and combining it with this structure generation idea would be a pretty unbeatable combo once Rust is further along and servers are on the full huge maps with semi-stable communities built up.