Marcus dicit se hanc coniugationem facilius intellegere quam illam.

Because se is the reflexive pronoun, and it refers back to the subject of the main verb, Marcus.

So:

• Marcus dicit se... = Marcus says that he...
• The he is Marcus himself, so Latin uses se

If Latin used eum instead, that would normally mean Marcus says that some other male person...

Also, se is in the accusative because in this construction it is the subject of an infinitive in indirect statement.

After verbs like dicit (says), Latin often uses indirect statement, also called the accusative-and-infinitive construction.

So instead of saying:

• Marcus says that he understands...

Latin says, more literally:

• Marcus says himself to understand...

That is why you get:

• se = accusative subject of the indirect statement
• intellegere = infinitive verb

This is one of the most important Latin sentence patterns to learn.

In English, subjects are normally in the nominative: he understands.

But in a Latin indirect statement, the subject of the infinitive is put in the accusative. So:

• se intellegere = that he understands
• literally, himself to understand

This feels strange to English speakers at first, but it is completely normal in Latin.

Because they are the direct objects of intellegere.

He understands what?

• hanc coniugationem = this conjugation
• illam = that one / that conjugation

So both are in the accusative.

Latin often leaves out a noun when it is obvious from the context.

So:

• hanc coniugationem ... quam illam

really means:

• hanc coniugationem ... quam illam coniugationem

In English we do the same kind of thing:

• this conjugation ... than that one

So illam means that one, with coniugationem understood.

It introduces the second part of the comparison after the comparative adverb facilius (more easily).

So the sense is:

• he understands this conjugation more easily than that one

Latin does not repeat everything. The full idea is something like:

• se hanc coniugationem facilius intellegere quam illam [coniugationem intellegere]

In other words, the verb intellegere is understood after illam.

Facilius is a comparative adverb meaning more easily.

It modifies the verb intellegere, not the noun coniugationem.

So the idea is:

• not an easier conjugation
• but understands more easily

That is why Latin uses an adverb:

• facile = easily
• facilius = more easily

If Latin wanted to say an easier conjugation, it would use an adjective instead.

Because they refer to coniugationem, and coniugatio is a feminine noun.

So the demonstratives must agree with it in gender, number, and case:

• hanc coniugationem = feminine singular accusative
• illam [coniugationem] = feminine singular accusative

This is normal adjective/pronoun agreement in Latin.

Not in this sentence.

Here illam is feminine accusative singular, but the context strongly shows that it stands for illam coniugationem.

So it means:

• that one
• or more fully, that conjugation

A learner might wonder about this because illa/illam can refer to a woman in other contexts, but here the nearby noun coniugationem makes the meaning clear.

Yes, but it is not unusual.

Latin word order is more flexible than English word order. This sentence is arranged in a clear and natural way:

• Marcus — subject
• dicit — main verb
• se — subject of the indirect statement
• hanc coniugationem — first object in the comparison
• facilius intellegere — the action and the comparative adverb
• quam illam — second half of the comparison

One nice effect of this order is that hanc and illam are separated and contrasted, which helps emphasize this one ... than that one.

Normally no. In a sentence like this, se naturally refers back to the subject of the main clause, which is Marcus.

So:

• Marcus dicit se... = Marcus says that he... where he = Marcus

If Latin wanted to say that Marcus says someone else understands it, it would usually use a non-reflexive accusative pronoun or noun instead.