From the Batcave to the Bunker, the Arrowverse has featured its fair share of superhero bases. The Fortress of Solitude stands out among the rest as a true base of operations. It has been utilized multiple times in Supergirl, yet the show's interpretation of the Watchtower has several features the Fortress lacks.
As stated in the name, the Fortress of Solitude is Superman's base and it's set in an isolated location, typically somewhere in the Arctic. Although convenient for someone like Superman and Supergirl to get to quickly, allies without their incredible speed would find it difficult to get to the Fortress. It's hidden location means enemies can't find it though, giving it that advantage.
The Tower succeeds where the Fortress fails: it allows easy access to allies of the Super Friends, while also hiding from villains. After Luthor Corp took control of the D.E.O., J'onn retrofitted a section of his building for the Super Friends to use outside of government oversight. Its location is kept a secret, with only members of the Super Friends and their allies knowing where it actually is. Due to this, Lena Luthor is able to go to the Tower whenever she needs without worrying about some super villain showing up uninvited.
The location not only provides ease of access to the Super Friends, but also keeps them close to the action. Since it's based in National City, it allows the Super Friends without super speed like Sentinel and Guardian to respond to danger in a timely manner. It also makes for a more believable secret base than the space-based Watchtower with teleportation features, adding a level of realism to an otherwise extraordinary base.
Although it may not have the extensive Kryptonian data of the Fortress, the Tower still has access to Earth's networks and satellites for whatever the Super Friends need. Along with this, the Tower has an ability the Fortress never had: it's mobile. Thanks to J'onn's design, the Tower can transform into a ship when needed, such as when the Super Friends required one to save Kara from the Phantom Zone. Hypothetically, this means they could also use this feature to move their base to another permanent location if the old one came under attack or was revealed to the public.
Overall, the Tower keeps the Super Friends close to humanity, something the Fortress of Solitude or the Watchtower never did. In other media the Watchtower has often been criticized for being a superweapon the Justice League could use against humanity should they turn evil. If the location or specs of the Tower was revealed to public, the Super Friends would likely not face backlash in the way the Justice League or Superman has for their heavily fortified, potentially dangerous bases.
Being close to the public also helps the Super Friends in their quest to act as heroes for the people. Kara and Kelly have each fought against social issues, using their positions as heroes to fight for those who do not have a voice. Due to living among the people, the Super Friends are seen as just that, people, rather than godlike beings looming over humanity. By allowing the Super Friends to work amongst the ones they've sworn to protect instead of isolated from them, the Tower succeeded in ways the Fortress of Solitude never could.