I will give my answer based on my opinion. Here is the list on Tibia.Fandom with the Charm points costs and differences between them:
Major Charms:
Looking at the elemental runes, we see that all of them only increase the chance of activating when upgraded to level 3. Levels 1 and 2 have a considerably higher chance, and level 3 only adds 1% more chance. This is also applied to all other charm chances. Every charm when upgraded to level 3 grants only 1% chance more than level 2. In practice, it may be that they are activated much more often, since we know how much of a difference this 1% can make. However, if you have few charm points, I don't think it's feasible to upgrade them to level 3, since the cost is too high and the return should be minimal. Level 3 was created thinking about players who want to do all the bestiaries in the game and have points to spare. However, even doing all the bestiaries in the game wouldn't make you have sufficient points to upgrade every major charm to level 3. In my opinion, there are only 2 runes that are really worth investing in up to level 3.
1. Low Blow -> Adds 1% chance to critical hit and this applies to all monsters in the box, not only one like the elemental charms, so let's say you are an Elite Knight using Sanguine Razor imbued with Powerful Strike. Considering you have 10% chance from the sword, 10% chance from the imbuement and 9% chance from the charm, it becomes 29% chance to crit.
2. Savage Blow -> Adds 4% critical extra damage. It's the same as Low Blow, but instead of chance, it buffs the damage. I think that both charms are equally good, I only put it on the 2nd spot because it is a new charm. But let's do some calculations. Using the same Elite Knight as before, he has: 12% critical extra damage from sword, 50% critical extra damage from imbuement and 44% critical extra damage from charm, it becomes 106% critical extra damage.
Using both those charms on different monsters will trigger more criticals, and the ones that has Savage Blow, it will do a huge spike of damage.
Those are the only 2 charms that are worth a permanent level 3 in my opinion speaking of Major Charms. You can take into consideration hunting for a long period of time in a particular place (like Ice or Energy Library for example) and level up a elemental charm to level 3 considering you will be killing lots of those creatures.
For example: You will hunt on Ice Library, creatures there are weak to fire, then you can upgrade Enflame to level 3 while you hunt there. But you need to make some calculations first, as resetting charms can be expensive later. I think it's much better to unlock more charms at level 1 or level 2 than upgrading a charm to level 3. You will be better having more options to use in all hunts, and specifically for places where there are more than 2 types of creatures, it will be more efficient to have charms at level 2 than a single charm at level 3.
Minor Charms:
Now speaking of Minor Charms, there you really have room and it's really worth it to upgrade them to level 3 because they increase the chance or improves the effect equally between all levels.
My options are:
1. Void's Call (Mana Leech) -> It increases the same percentage as lower levels, and we all know how mana leech is effective on hunts. You will always be using a mana leech imbuement and it is guaranteed to activate every time you hit the specific monster that has been assigned to it.
2. Vampiric Embrace (Life Leech) -> The same as Void's Call, it's a guaranteed buffed life leech stacked on your items and imbuements, also the percentage follows the same pattern as lower levels.
Optional Minor Charms for specific hunts (no ranking as they are situational):
Gut -> Gut is a charm that works mostly for profit. When you are hunting for profit (imbuement items), it will simply make the creature drop more of them. I say it is optional because I rather have more mana and life leech on my harder hunts and I would only use it if the hunt has more than 2 types of monsters.
Void Inversion -> You have a chance to get mana instead of losing. This one is really good against monsters with mana drain (like Hand of Cursed Fate), and the amount of chance to make it trigger is worth the level 3. It increases the chance by 10%. I also say it's optional because not all hunts have creatures using mana drain, then you would not use it on most of hunts, but if you have a creature that does mana drain, then you can use it as it's effect basically works like a mana leech. It prevents you from losing mana and instead gives you mana back.
Fatal Hold -> The same as Void Inversion, you are not always hunting creatures that flee while on low health, but it is really good to upgrade to level 3 because it increases chance to trigger by 15%, that means creatures will not run so often while you are hunting them.
Conclusion:
And this is my list. This is not a definitive answer, as each person has their own opinions and insights into the feature. Some may think it's better to have that additional 1% chance on their elemental rune, others will prefer another options, but I hope I've helped you to analyze the options and also calculate if it's worth it for you. I think that level 3 is only a plus, but it's not mandatory like level 2 for example. I don't think it's worth to keep resetting the charm points all the time since it will become more expensive with each level that you get.
I really hope that this information is good for you :)
Thanks!