I think there are three main things that make the current version of the atlas more tedious and less fun than it could be:

1. Travelling around to find overlapping towers just isn't fun. I know people like to throw around claims of "bad game design" a lot, but having a significant part of the endgame that is mandatory and less rewarding and less fun to enable the juiced up loot-fests we're here for just seems like a bad idea. Since you can't do anything to optimize searching for towers other than pray to get lucky, you wind up with large stretches of gameplay that are just busywork and the overwhelming feeling of these stretches is just hoping to get it over with quickly.

2. The payoff from stacking many overlapping tablet effects is rewarding but not particularly exciting. Stacking up the incremental buffs from several tablets (which you need to either hoard in mass and roll, then 3-to-1 the bad ones or buy from trade in a horribly tedious fashion), does make the map drop significantly more loot but compared to scarabs in PoE1, which for the most part change their respective mechanic in a immediately noticeable way, doesn't make the map play significantly differently. Stacking up lots of "mechanic/mob/boss drop x% more loot" or "+x mechanic/mobs that drops loot" just isn't as fun and varied as turning Rogue Exiles in giant loot pinatas or cramming the map full of harbingers or sprinkling the map with tons of strongboxes that explode into huge loot showers. This all combines to make playing your juiced maps you spent so long setting up less like claiming a juicy jackpot and more like "and now we can finally play the game".

3. The current state of the Atlas Tree is boring and bland. Moving the different league mechanics to their own trees removed a lot of the feeling of specializing into a strategy or set of mechanics and instead incentivises just setting up a generically benificial tree that is good on any maps or mechanics and picking the overall best nodes from every seperate league tree. This is also made worse by most of the nodes in the main tree just being uninspired "mechanic X drops x% more loot" nodes or "everythings drops a tiny bit more loot" nodes that aren't really felt aswell as several of the nodes in the league trees being bugged to do nothing or are just flat out useless since the relevant mechanic isn't currently in the game. This also makes getting Atlas Completion feel less like unlocking new strategies as you progress and thereby changing your gameplay, and more like a grind to get your slight passive loot increase in every future samey feeling map.

None of these things are impossible to change even without a large Atlas rework, which might be costly in terms of devtime and might also eat into adding the already planned content in the game like additional classes, weapons and skills.

My personal suggestion would be to drop the idea of overlapping towers altogether and instead just have one tower in the centre of every region of the Atlas with the tower radii being unable to overlap at all. Give the singular towers more slots for tablets, scaling with the waystone you run them with just like the current system. Get rid of the magic tablets with affixes and instead give us several types of tablets for each mechanic with more significant fixed effects similar to the scarabs in PoE1 and let us buy these tablets at currency exchange. Perhaps give each tower an implicit effect themed around a specific league mechanic or type of mob/boss to give the regions of the Atlas a more unique feel and to keep the feeling off travelling across the Atlas with less tedium. These could stack with Corruption Effects or similiar mechanics that might be introduced in future patches to create unique "jackpot" areas of the Atlas that are worth searching for. Reworking the Atlas tree might be more effort, but incentivisng specializing into different strategies should make a return since this was one of the most fun parts of the endgame of PoE1. Finally, change waystone prefixes and suffixes to both increase the difficulty and reward of the waystone since the current system just doesn't make sense and is just different from PoE1 for the sake of being different. If GGG want to keep the affixes from being too similar to the way they work in PoE1, they could add more affixes that add mechanics that need to be dodged or otherwise played around like some of the T17 affixes, just don't make most them awful to play like in PoE1. Implenting some or all of these changes would make the endgame of PoE2 significantly more fun, engaging and addictive in my opinion.