Zana is terrible. It is a shitty chaos sink and ends up being not worth it for a large portion of the playerbase. League stones were cumbersome and clunky in many ways, but offered a very pleasing, self tailored, and easily sustainable experience for a lot of people. Though, some kind of system similar to like how skill points or Ascendencies would have been better IMO. As you level Zana you unlock points to put in a tree and eventually can have 3 (or more) permanent leagues always. With some of the "better" ones as far keystones only available at like level 7. Put in a regret cost to respec and you're fine.
Instead we get this crappy Pantheon system coming in 3.0. If they don't seriously tune this, it is going to be essentially worthless. Oh, 30% to not bleed? Why, thank you GGG. How could you have guessed I'm a complete noob and don't have a bleed immunity flask!
I kind of wanted to say this before I start debating your solution. I think that the Legacy league version of Zana is absolutely terrible. The pre-Legacy version will hopefully make a return in 3.0 (just hoping, have no evidence to back it up), and I'm guessing the change is just a placeholder since Legacy league is largely just Zana mods in any zone.
I feel like your suggestion is already similar to the current Zana system. You start out with no mods you can add, as you level her up you gain access to different mods. The only difference being you want the mods for free, and that can't work out. If you are getting the mods for free, then you are more than doubling your drops for zero additional investment (people run the master mission for the free map anyways).
The true issue with Zana is that the mods themselves just aren't rewarding enough. If you look at the Legacy league version, there's no reason to even use the mods unless you have extra chaos laying around, they just aren't worth it. If you look at the pre-Legacy league version, again same issue. You run beyond for extra xp/drops, and I can assure you the chaos is well spent. If they were to include breach and perandus at reduced league specific drop rates (coins, splinters, league specific uniques) as well as revamp the other mods (bloodlines/nemesis? absolutely no reason to spend chaos on those) we'd have a really nice system going and I'm sure they can be balanced to where not everyone was using the same mod for every map.
You have to be careful with this type of stuff though. A lot of these league mechanics make it to where you get a large increase to drop rate and experience. If you make these too accessible, it ruins the economy. If they are too underwhelming, it's a useless feature.
I do agree with you that the pantheon system is underwhelming. I feel like GGG hyped up the new system way more than it should have been. I can only see very few of the pantheon nodes being worth it for niche builds, and the flask generation node is just bonkers. I think the real issue is that you get the pantheon nodes for just playing the game. There's no additional content to complete, and therefore no additional challenge, so the rewards can't be very strong. When you compare it to lab, lab is something that you can completely skip, but the rewards are just too juicy to pass up so it almost seems mandatory. I wish pantheon came with a similar challenge.