Oh my goodness, did you create a meta puzzle?

Are you QuantumTwinkie????

My prefix describes some folks you might know,
who shun convention wherever they go.
They're not rebellious, they don't break the rules,
but you might find them ... strange in the things that they choose.

These could be QUANTs (ie. quantitative analysts, ie. dataheads). These people tend to focus on the results and insights that the data tells them is true, rather than agreeing with "conventional wisdom".

For infix the first, I have a bad habit
I am guilty myself, I have to admit.
For this awkward thing manifests when I speak,
And for many more too, especially the meek.

When you stutter, you say the word UM.

Next infix is easy, you're doing it now,
You don't think about it, but you do it, somehow.
Take that and swap height with width, you are almost done,
Infix 2 is now complete, and the suffix has begun.

I definitely am THINKing right now, and I don't think about me thinking (FYI, that's metacognition, and we're not going there). When I swap Height with Width, then THINK becomes TWINK.

The puzzle's almost over, this is your destiny
Just take the apple and throw it out, and closer you will be.
Take what's left, chop it up, and give it to The Pope,
If you have his help, there is still some hope.

Not sure about the first part, but you mentioned that the Pope was Latin. the suffix IE is a Latin phrase that means ID EST (that is, it means "that is")

Good luck with this puzzle, give it your best try.
If you figure out my name, then tell me. Who am I?

Putting it all together, you get QUANTUMTWINKIE, which would be a really amusing homage to your supposed "nemesis"!

Oh my goodness, did you create a meta puzzle?

Are you QuantumTwinkie????

My prefix describes some folks you might know,
who shun convention wherever they go.
They're not rebellious, they don't break the rules,
but you might find them ... strange in the things that they choose.

These could be QUANTs (ie. quantitative analysts, ie. dataheads). These people tend to focus on the results and insights that the data tells them is true, rather than agreeing with "conventional wisdom".

For infix the first, I have a bad habit
I am guilty myself, I have to admit.
For this awkward thing manifests when I speak,
And for many more too, especially the meek.

When you stutter, you say the word UM.

Next infix is easy, you're doing it now,
You don't think about it, but you do it, somehow.
Take that and swap height with width, you are almost done,
Infix 2 is now complete, and the suffix has begun.

I definitely am THINKing right now, and I don't think about me thinking (FYI, that's metacognition, and we're not going there). When I swap Height with Width, then THINK becomes TWINK.

The puzzle's almost over, this is your destiny
Just take the apple and throw it out, and closer you will be.
Take what's left, chop it up, and give it to The Pope,
If you have his help, there is still some hope.

If you take the word DESTINY, and remove the Big Apple (New York, ie. NY), you get DESTI. This is a scrambled form of the words ID EST, a Latin phrase (remember the Pope?) that means "that is". The short form of ID EST is the suffix that we are looking for: IE. Thanks very much to @kayzeroshort for discovering the wordplay in this clue!!

Good luck with this puzzle, give it your best try.
If you figure out my name, then tell me. Who am I?

Putting it all together, you get QUANTUMTWINKIE, which would be a really amusing homage to your supposed "nemesis"!