Based on the well-reasoned arguments that I've been reading from CharlesSprinkle and ComicIDIOT above, it sounds to me like having /town spawn, /spawn, and beds is the best compromise. But if people can carry around beds and use them to set homes in mines, why don't we just allow regular Essentials /home and /sethome? Thus, I amend my suggestion to allow /town spawn, /spawn, and /home slash /sethome, but no /tpa.
Although I am a strong advocate of keeping the transportation system as it is in the current map (all teleport commands, but also more conventional transportation such as roads and trains), I feel like the suggestion KermMartian makes would be the best compromise.
/Spawn seems essential to me, since spawn is often used as a social hub where people meet up.
/town spawn this is one of the least useful teleport commands if you ask me. I wouldn't mind it very much if this wasn't available in 1.9
/home One of the most useful commands! I use it for instance when building tall buildings, to get back up onto the wall when I had to go down to get more blocks. Also very useful when moving items into a newly built vault / storage. I think it would be one of the worst commands to take away.
Additionally, if it would be possible to attach a cost to each /sethome, I think that would be fair to limit it's use.
/tpa I really like this command to quickly group up with other people and do things together. Afterall, that's why we play on a server, so we can do things together. Taking this away would create a bigger threshold for people to group up in my opinion.
That being said, I would be willing to compromise and give up access to /tpa as well.
Conventional forms of travel
I would love to see even more roads across the landscape, connecting towns to other towns and spawn. If done right, it would also be possible to facilitate travel via horses this way.
Railroads provide another fast way to travel, which can definitely make travel easier, but they do have to function as intended. There have been a few problems with the rails in the current world, which dissuaded people to use them for quite some time.
Rails: I'd like to get away from 1.8's rail system. Nothing so far up, it's all at ground level, which would at that point give a reason for bridges to exist, not only for people to cross, but for the trains as well. I also think the players should build the rails system up. I think from spawn, it'd be nicer instead of just having it go the 4 directions, they should go out to the nearest town in that general direction. Each town would have a train station of sorts to receive and send off carts. The tracks for each one would need to be the same, but the building itself should be up to the town members.
I agree with this for 100%!