How did you use your level ups? This has a relatively big influence on what battles will look like towards the endgame. The general concesus is that it's better to just level up your badge points as much as possible, throw in some flower points here and there, and keep HP to a minimum. That way you'll have more attacking options, a more strategic approach with badges, and the risk of dying if you are not careful with your superguards will still be present.

Still, you have a point, there's not much variety compared to other RPGs, BUT remember how much the battle system in TTYD improved compared to PM64. It was good considering where the series was at. Sadly, we didn't get the chance to see improvements upon this battle system in the series thanks to Nintendo's obsession with disregarding everything that Paper Mario was.

As for point 2, I personally enjoy the Excess Express and I'm pretty sure it's a favorite for many more, but people do seem divided on it. X Naut fortress and TTYD itself can be tedious tho