I'm sorry , but I disagree.
The badges were handeld very well in Paper Mario 64. One major thing to know about this game is that it has a level cap , compared to TTYD. So you can only get a max of 30 badges points , and a lot of the more powerful badges like Power + end up costing 20% of your badge points.
Of course , you're always going to have badges that are better than others. A perfect balance is impossible. The only badge I ever found to be on the more OP side will be the infinite jump one , because you always get it very early on , and it doesn't cost that much. However , they also balance it against bosses by giving a cap of maximum jumps , so you can't just cheese your way through.
You of course have the boosting strategies , by pairing up jump boost and the infinite jump badges , you could do a loooot of damage. But honestly , if you managed to boost 3 turns in a row without attacking , I think you deserve the extra damage.
There is also the fact that in PM 64 , Partners don't have HPs , so you can't let your partners constantly tank everything.
However , I get where you're coming from if you're talking about TTYD.
This game , imo , has the shroom badge syndrom from Superstar saga. By default , the game isn't too hard , but specific badges combinaisons can completely ruin the difficulty of the game , especially for the post game content.
The biggest example of that are the danger/peril Mario strats. A badge can boost your attack whenever Mario is at 5 HPs or less , or 2 HPs or less. The main issue is that you can farm them at the casino , and one of the NPCs of Rogueport can make it so you're permanently at 5 HPs. On top of that , you also have badges that increase evasion at low HPs... Yeah , you get where I'm getting at. This strategy make the 100 pits trial a joke , unless you get royally RNG screwed.
And the worst part is that TTYD doesn't have a level cap , so you could pretty much invest everything in BPs and FPs , and ignore HPs for the most part ; Not counting the fact that Partners can tank for you , and that you can increase their HPs by upgrading their rank.
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However... I feel like it doesn't make the badges badly designed or flawed by default. The strategy I mentionned is something very specific that need grinding , and isn't something the common player is going to do.
I think that the vast majority of badges are balanced , and even the OP ones have drawbacks.
I'll agree on the fact that in TTYD , you're really encouraged to focus heavily on FPs and BPs starting at mid game. Early game , after one or two HPs level up , you're good , you could defeat most of the bosses. But after that , you probably got a lot of badges , and most ennemies won't go down with basic attacks , so investing in those two stats become very tempting.
But in the end... It's less that the badges are overpowered , and more that IS didn't give us a proper level cap to balance it. TTYD is the worst when it come to grinding , because getting a level up in that game is a way bigger deal than a level up in a Mario and Luigi game or SMRPG. BPs and FPs change your strategy a lot , and you can quickly get overpowered. You can also farm thanks to these lovely flowers , so it doesn't help :
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So in the end , it's less a problem of core game design when it come to badges , and more a problem of level capping. At worst , a few select badges are too powerful for how little they cost , but this is something that can be tweaked.