General rule of game design for influencing a player to not abuse some kind of utility is to somehow deincentivize its use or to incentivize the use of something else as an alternative.
For example, in World of Warcraft when the Cataclysm expansion released the developers remade a couple of the older capital cities with new textures and layouts. However no one would ever see them because all the players would prefer the previous expansion's capital city of Dalaran because of the convenience of its portals which lead pretty much anywhere the player could want to go. They added incentive to see the shinier, newer cities by removing the portals in Dalaran.
So, the question is what can you to either incentivize going to normal towns, or deincentivize going to the town you can portal to?
One option is the add a timer on being able to go to the portal town, but often times you will end up just having a player AFK to wait for the cooldown to be over so they could go there. It would be ineffective and make the player feel like you're being heavy-handed in limiting their use of this "super awesome portal town"
Another option is to have it recharge in some way. Basically forcing the players to do something (as mentioned before, walking steps or killing monsters) to slowly recharge the portal. The downside to this is that players can sometimes think of this as tedious or grindy in some fashion and be rather off putting.
Another possible solution is include some kind of purchasable item that allows the player to teleport to the portal town. Perhaps these can be most commonly found in normal towns or rarely as treasure. The downside here is that players will likely overstock on them early if they're cheap enough so they won't have to buy them ever again or they will feel that obtaining them is too difficult/grind-focused if they're too rare or expensive.
Yet another possibility is to somehow deincentivize use of the portal city by incentivizing normal towns with a reason to go to instead of the portal city. The most obvious solution here would be access to vendors or the quality of their items; for example the portal city could be way behind the "technology curve" of normal towns when it comes to the quality of items you can purchase there. The downside here is that you would have to give a completely unrelated incentive to actually go to the portal town (for example, the side quests you mentioned, special fun items, etc.).
A final solution I can think of is to only allow access to the portal city from special locations. Examples include save points and other more important towns. This would make the portal town something the player looked forward to in addition to whatever method is used to reach it. Putting the portal in each major town would solve incentivizing the player wanting to go to both places, so long as each location (the normal town and the portal town) had different reasons for the player wanting to visit them (such as better items in the normal towns, but side quests and some other special utility such as fast travel in the portal city).
In short, it all boils down to incentives and how to nudge your players to do what you want them to. Another thing to remember, if you're afraid players might think something is so powerful/useful that they would always use above everything else, chances are that it is.
