... Are you skipping enemies in areas rather than fighting them? Genuine question. This sounds like the result of you being underleveled. Of course Shroob Castle is difficult, it's the end game level. These are enemies you're supposed to be in your 40s or so when fighting. If you want to be underleveled for the challenge, that's absolutely your call to make (and I've even tried to do so in RPGs before), but it doesn't make the game unfairly scaled if you are struggling in an end game area at level 25.
Everyone on my team has EXP in the mid to late 30000s range (Mario has 35763 EXP, Luigi has 35757 EXP, Baby Mario has 37285 EXP, and Baby Luigi has 37261 EXP), and do you want to know how much EXP you need to reach level 31? Mario and Luigi each need 50902 EXP to reach level 31, and their baby counterparts need 53374 EXP to reach level 31. The amount of EXP I have nets me a level of 27, so I was actually at level 27 when I beat the game on an emulator. Charriii5 was at level 23 when he got to the final area. I only skip the enemies that I know I'm going to lose to, and an example of this is a group of five Bob-ombs as Baby Mario and Baby Luigi. Also, it's not just the final level. there are several points in the game where I feel like I'm underleveled. Also, you want to be on par, maybe a few levels lower than the final boss. Well, in Elder Princess Shroob's case, that's level 30 for her first phase and level 31 for her second phase. The highest level enemies are level 28, and those enemies are Shroobsworth, Intern Shroob, and Ghoul Guy. Meanwhile, the regular enemy with the most HP, the Shroob Rex with 200 HP, is level 27.
On the topic of the Shroob Sisters, Princess Shroob, who is level 29, has 3000 HP (thankfully, she only has 1700 HP in the European and Japanese versions of the game, just over half the HP of the American version). I've only been using Bros Items when fighting bosses, and even then, I only use the most powerful ones I have at the moment because the first few Bros Items kind of suck, especially when I get the Trampoline, Copy Flower, and Mix Flower. But even then, it's not like it'll be super useful if I have a 75% chance of screwing up an input with something I have a limited quantity of. Granted, I have an Ulti-Free Badge, which costs 90 beans, but because there aren't many beans in this game, you can only buy one, and this is your only way to keep more Bros Items.
And the worst part about this battle is, you don't even get experience for it. You realize that there's one more fight after this, right? One where I could use the stat boost, because Elder Princess Shroob has 3500 HP in her first form. That's 500 more HP than her sister as well as her second form, which you don't get to heal for: you beat Phase 1, you go straight into Phase 2, meaning that altogether, she has 6500 HP. And do you know how I know that even the developers agreed that she had way too much HP? In the European and Japanese versions of the game, she has 3800 HP total (1800 in her first phase and 2000 in her second phase). Only 300 more HP than her American first phase, which, by the way, is almost twice as much HP as the non-American first phase. And honestly? Thank God for the Trampoline, Copy Flower, and Mix Flower. Because otherwise, I don't know how the game expects you to beat her second phase. You have to damage her, same as any other enemy, right? But in order to do that, you have to damage her crown to deactivate it. Okay, that's fine, but in order to even be able to reach the crown, you have to take out her legs. Keep in mind that each body part has its own HP; each of her four arms has 200 HP for a combined total of 800 HP for the arms alone, way more than any regular enemy in the game, the legs which have 400 HP, also more than any regular enemy in the game, and the crown has 200 HP, the same amount as a Shroob Rex, the regular enemy with the most HP. Also, each body part regenerates after three turns, so get in as much damage as you can before then.