Your post seems to imply that it's extremely different in a lot of ways. That's what I see, anyway.
Ok I'll dissect it for you. Here's mainly why I see the PM series existing with the M&L. And yes to answer your question, I do see it different enough.
The paper mario series is a turn-based RPG game that stems from the Super Mario RPG origins.
1. The battle system is one proof of that.
In most games, you basically attack using your weapon (well in this case your attack actions (Jump, hammer whatever) and hope that you inflict enough damage.
However, you must also expect to be attacked at all times and hope that your defense is high enough for you to survive (as you cannot dodge but only defend)
The partner systems stems from that too. They have their own basic attacks and special attacks that uses FP.
The way the story is made also stems from SMRPG. Haven't you wondered why in the PM series, you always have to catch seven stars, or something similar to that extent? Yeah...
Now here's the funny part. The M&L series completely throws that formula out the window.
1. Sure the battle system is turned based and has the action commands and whatnot. But the fact that makes it different is how the battles are handled. It's innovative.
Basic commands requires timing to perform like the PM series but advanced action commands requires more skills to perform as you must imput the right button combinations AND time to get it right. If you miss, you can completely miss a whole attack. It's more of a gamble.
Furthermore, you can dodge. Completely dodge and/or even counter-attack attacks which makes you feel like you're more in control of the situation, while in the PM series, you're not.
2. Oh yeah, some of the battles also completely break away from it's formula, (The giant bowser battles are examples of that.)
3. What also makes this game rather known is it's completely humerous storylines. It makes the series less stale and it can become quite unpredictable. The characters are rather lovable and they actually have more personality. You may think that it doesn't matter but it's what makes this series rather unique and different and it's also what makes the experience rather different than the PM series.
The series that you've shown me are barely different. That's true. But do not consider the same with the PM and M&L series as while they are RPG games, they are different enough.
Tbh, If the SMRPG continued with the PM series, I would have agreed.