I think I've finally had a... what is it called? epifanny?
The one thing that everyone in this thread has agreed on is that if the players had the proper in-game resources to skip the desert, such as teleportation or Overland Flight, then skipping the desert would be absolutely no problem. So, the issue isn't really whether or not the desert is relevant. If it was the relevance of the desert that was important, then there should be objections to any means for skipping the desert.
No, the objection boils down to the fact that the group does not actually have the in-game sanctioned resources to skip over the desert. I tried to make a plausible one by summoning a mount, but, at the end of the day, the critics are right, it doesn't really skip over the desert. And, really, there's a great point here. If I want to travel to Las Vegas on foot, the desert is going to be relevant.
But, that presupposes a certain playstyle where the physical reality of the game world is such that only the DM can determine when parts can be hand waved. It's very much like an MMO game world. If I want to travel in an MMO, I have to travel through each of the regions in between, risking being attacked or whatnot on my way from start to finish. ((Note, I'm not trying to bring in a video-gamey canard here, just making an example))
I don't, and I get the feeling that Pemerton doesn't, feel that the DM should have the sole say in what parts of the game can be hand waved. Yes, it would likely be best had we had the proper in-game resources, but, we didn't. But, since we're playing a game, I don't feel that the players need to be forced to play out the consequences, when they don't want to play out those consequences. Most of the time, players will want to play out the consequences. Your ship sinks and you make it to the desert island - presuming buy in from the players, you are good to go.
But, I also don't have a problem with the players having strong enough opinions to say, "Hey, y'know what? Let's skip over the Castaway scenes and I don't even have a volleyball - can we just get to the part where we leave the island?" Obviously, some people do.
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On a side note about relevance between the desert and the siege. Imagine for a second that the party does have a teleport spell. Now, they've arrived in the city with the city under siege. The desert in this scenerio is entirely irrelevant. Is the siege still irrelevant? I would say no. If nothing else, the players must achieve their goals before the siege breaks into the city. Plus, the presence of the siege is going to radically change the reactions of the NPC's. A peaceful city is going to be completely different than one under siege. However, the presence of the desert around the city doesn't really have much of an effect - the city happens to be in a desert and that's about it. It's entirely background and has very little impact on play.
That's why the siege is relevant. It's always relevant no matter what the players do. Even if they just fly over the siege, the city is still under siege. But, the desert? Doesn't really matter a whole lot. The nomads are still out there somewhere but, since they aren't linked to our goals, who cares?
Can you make the desert relevant by forcing the issue? Oh sure. The nomads have recently stolen the MacGuffin and we have to go back out to the desert to find it. Fair enough. Although, again, we couldn't have known that at our arrival point in the scenario. We had to go to the city first to find that out. I suppose we could "randomly" meet that group of nomads on our way to the city, who just happened to be the nomads that we need to meet, but, that's about as contrived as you can possibly make it. Our random Planar Travel destination results in our landing in exactly the right place to meet the nomads? If this was a novel or a movie, I'd stop right about there. That's Syfy level writing.