More ideas:
-Roads and RailRoads should cost money, like done with Shaft Mines and other improvements. It would avoid the inverossimile spam of it around our lands and AI's.
Discussed this already. Since pre-superhighway roads were as often as not built not by order from the capital, but by locals using local materials (leading to very widespread differences in road quality outside cities, I might add) I don't see why the central government (you, the player) is being charged money for an improvement that is done on a local-purchase basis.
- The civics should be changed DESPITE the player and AI's will, using the Revolutions mod or maybe the new events. This would reflect situations where societies' intellects know what would be the best type of state, but can't change how the things are.
- Following this idea, a new Great Person could be created: the Great Revolutionary, like Lenin. These guys can give the players the possibility of change civics accordingly their will.
I don't know - it might work in, say, Thomas' War, which is already Python-heavy and has a couple extra GP categories, but in RoM, which on most machines is already unplayably huge at its upper end in the modern era, I really think that you're running into the problem of realism vs. system resources.
- Open Borders Division:
- Civil Open Borders (Scouts, Workers, Merchants)
- Commercial Open Borders - Trade Routes
- Military Open Borders
The differents levels of these would change the

caused by spies getting caught.
Absolutely, though I'd simplify "civil open borders" and "commercial open borders" into one category. Diplomatic hierarchy would be something like this:
Cross-Border Trade (your civil/commercial) -> Open Borders (your military) -> Defensive Pact -> Permanent Alliance
Each stage would require the others to be complete. This allows something like the real-world Holy Roman Empire, where imperial troops can march pretty much where they want within the borders of the empire, and trade occurs inside the same zone, without creating a "Holy Roman Empire" state where no such thing really existed.
- Military maintenance should much more expensive, and armies size food-production limited. This would increase even more the battle experience importance, as well the military strategies. It also would cause a much more frequent change of cities' ownership, like real history.
Civ4 already has problems in the medieval era not linking population base and food production to military size. Honestly, I think what you're asking here would require a serious re-tooling of the way it handles things, similar to Civ2's home-city system. It's probably doable, but is it doable within the framework of RoM, or would it need a ground-up mod?
- The trade routes could be explicitely player-designed, I mean, manually. This would stimulate even more the exploration beyond borders, and the discovering of new routes, more cheap or not. When I say this, i'm thinking at the portuguese efforts at the Middle Age to discover new paths to India, in order to get the valuable resources there, without depend on Venezian or Genovian merchants.
This seems reasonable to me, though I'd want a button that just says "optimize" to let the computer do my thinking for me. Frankly, RoM takes long enough to play through without me going "if I switch this route from X to Y, what will change?" for five trade routes per city.
A lot of your proposals add to realism, but not to playability. RoM is already borderline unplayable on a lot of machines because of size and scope - making it
more bulky is not the answer.
Regarding resources becoming obsolete - I vote against it. Stone, I've explained elsewhere. Obsidian is borderline, but then, I consider it borderline as a resource. It has exactly the same applications it did 500 years ago, and is widely used for surgical implements (not as widely as steel, but widely enough that I know about it and I'm not a surgeon). Horses aren't as widely used in, for instance, agriculture or daily life (and are outdated by trucks, not commuter trains, which means Mechanized Transport, BTW), but they're still both agriculturally and economically significant in large portions of the world - Kentucky and the Arabian Peninsula, to name two places. Basically, while they're not used in cities near as much as they used to be, they still have uses. If hemp and tobacco are included, horses fall in the same category of "luxury resources" in modern times.