Then again, with roads between cities you may not be able to order a road being built between a town and the border with a neighbor. What if I want that because I plan to invade?
If you're not trading with your neighbor, you're not going to have a road. I like this speedbump to initial conquest -- players have a little more time to build up because initial contact is going to involve either trade and diplomacy or an army crossing a gap in the road network. Building a road would slow down an initial army; the road is for reinforcements. Not having a road built when you take the first city gives the defender a chance to strike back before you reinforce.
You often hear about the "slippery slope" in games, particularly strategy games. This is the problem of the player in the lead getting advantages for being in the lead. The slippery slope is a natural part of this sort of game -- players pursue goals in the game precisely because they provide advantages in the game, and this is what drives the conflict. But it's also good to have "grippery slope" mechanisms that allow a player whose fortunes are poor to claw their way back.
This is particularly true in the early game, or the early part of a war. It really sucks to feel like you lost just as things were starting and most of your gameplay experience was just an inevitable, helpless descent following your initial defeat. I'm sure there will be trump cards in the magic system, and probably some in other systems as well, but I think there's also a benefit in organic roads giving defenders a slight circumstantial advantage in responding to that first lost city.
I see your point though even though I disagree it will distract from the game. I do not feel like roads are secondary though. In an empire management game roads are vital to the economy. They are not things of secondary importance.
The roads which are economically important will arise as a function of the economy. This is exactly the need that organic roads fill, blending roads as an economic force and roads as an economic indicator. What you are objecting to is not a lack of economic roads -- for there is no such lack -- but a lack of military roads, and more specifically (since the economic roads also have military value) to a lack of those military roads which serve no economic purpose.
Direct road-building decisions are entertaining in some games, but others either wisely avoid them or are hampered by them. I think Civ 4 would be improved if roads and especially railroads worked like harbors -- build a connector building and join the network. (Mind you, Civ 4 is pretty committed to the worker system and a lot of other mechanics tie into it -- movement is balanced on the assumption that nations will develop carpets of roads, slave-taking is contingent on the presence of workers outside cities, other improvements require workers to build, and city growth is balanced for worker production -- so it wouldn't be a trivial change.)
As far as Elemental is concerned, there is a particular situation when this problem would supposedly come up: the player wishes to speed up military movement along a path which does not correspond to intercity trade. Of course this will happen, but when it does, the player will have other options which are more rewarding than army-built roads. General fast movement can be accomplished through assembling a fast army (e.g., cavalry, pathfinder leader, etc.), which uses the recruitment system, which is featured gameplay for Elemental. More broadly, magic and crafting have the potential for a diverse set of mobility solutions. In the early game, a typical gambit allowing fast army movement might be a cheap forestwalking charm, or a single capable hero with a flying broom. In the late game, a powerful empire could use an expensive spell to establish a gate from a newly conquered city to a built-up recruitment center (or to another dimension, permitting deployments of summoned creatures). (SotS is worth a look for mobility ideas. Each of its six factions has a different means of travel between stars, and only one of them (Zuul) is analogous to road-building.)
If you've ever played MTW2, you know what a chore it is to build watchtowers. Watchtower building doesn't just tie up units and drain upkeep and construction costs, it's also something annoying that you have to remember to do every turn. This was excised in ETW in favor of a system where you get the benefits of watchtowers automatically, and it's an incontestable improvement. By contrast, roads in MTW2 were treated as economic buildings in settlements which -- as they were upgraded -- provided roads to other settlements nearby. There wasn't a way to construct roads to nowhere, and it never felt like a lack. Organic roads in Elemental would be similar, although I see them as upgrading automatically -- particularly since the main reason not to upgrade roads in MTW2 was simply forgetting to do it (and kicking yourself when you realized you'd been neglecting the roads). The real gating mechanism for road upgrades in MTW2 was population/settlement size class, which corresponds nicely to possible Elemental criteria based on prosperity and trade.
Whatever may be of that, would it not be great if there was a system where the road fairies laid down roads between cities and to have the option of the army laying down roads wherever else it sees fit?
No. Once again, army-based roads only compound the problems of the worker-road system. The presence of the option will not be benign; either the player who does not use army-built roads will be at a disadvantage (creating an incentive to use this undesirable mechanism), or army-built roads will not confer an advantage, in which case the game will be weighted down with a useless, tedious, and ultimately illusory option.
I also want to object to dismissing abstraction as "fairies." Elemental, when finished, will abstract a lot of things that could, in theory, have been the subject of detailed mechanics. Abstraction isn't harmful in itself, and it's also not absurd in itself. There may be some abstracted things which happen because of fairies, but roads are not among them. A fairy-related spell for rapid craftsmanship might be nice to have, but the crafting system in general shouldn't be interpreted as "you design the item and then fairies make it" just because you don't swing the hammer and quench the blade manually. Similarly, there might be a spell that lays down a fairy road which allows swift travel but only lasts a couple of turns and risks deadly random encounters, but that doesn't mean there's any point to saying that organic roads in general will be constructed by fairies beyond baseless denigration of the organic road concept. Organic roads won't be paved by fairies any more than fairies will cut the timbers for automatic starting-level city walls.