The duration of space battles is always going to be weird in a real-time grand strategy game. If you think about it, it's not actually all that believable for the ships to be sitting there with weapons that only fire a few times a day or less, taking weeks of continuous fire to kill each other. But if battles resolved in less than a day, the player would experience them as instant, which also doesn't feel good. Contrast with more traditional turn-based 4X games, where the concept of time is flexible and the battle can take place in a cutscene.
Does anyone even use Juggernauts? They can't join fleets, they're extremely limited in terms of outfitting them forcing you to use strike craft, they are used as shipyard even when in transit/in a bad position with the ships being spawned wherever the Juggernaut is at that point and often simply remaining there rather than attempting to join their designated fleet, their auras are completely useless for the most part, AND the juggernaut is incredibly slow so it can't keep up with other fleets.
Juggernauts by almost all metrics, aren't worth the fleet cap one has to spend on them.
I don't think the problem is with Juggernauts themselves, so much as the context in which they were added to the game. They're not supposed to be just mega warships; we really don't need to go past Titans in that respect. Instead, they were supposed to support the logistics of a large mid-game fleet while it is on campaign. The trouble is, the way the game is designed, the logistics are already trivial. There's no concept of military units needing supplies in Stellaris, which already limits the importance of logistics compared to other Paradox games: we're only talking about repair and reinforcement. Inside your own territory, in the early game distance matters, but in a mid-game context you have a network of shipyard+gateway systems to the point that the physical sprawl of your empire is no impediment any more; it's almost impossible for any inferior enemy to conduct a hit-and-run campaign, since you can bring your entire power to bear on any given system in a matter of months (or even quicker if you don't mind taking jump penalties). Outside your territory, you're sometimes a little more limited due to lack of gateways, but even then, you capture shipyards as you go, so it's not that costly to park your doomfleet for repairs/reinforcements.
In the context of logistics as they actually exist in Stellaris, the only way you could make Juggernauts a big deal is if they literally had the functionality of a mobile gateway (which would make obsolete the Juggernaut's ability to build ships directly). Trouble is, if you did that it would not only make them 'good', it would be the final nail in the coffin of any sort of notion of galactic geography being important in mid-game/late-game warfare.
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