Το μεταπτυχιακό μου είναι δύσκολο αλλά ενδιαφέρον.

Literally, it breaks down as:

• Το – the (neuter singular definite article)
• μεταπτυχιακό – postgraduate / master’s (program/degree) (neuter noun here)
• μου – my (unstressed possessive pronoun, “of me”)
• είναι – is
• δύσκολο – difficult / hard (neuter singular adjective)
• αλλά – but
• ενδιαφέρον – interesting (neuter singular adjective)

So literally: “The postgraduate (degree) of-me is difficult but interesting.”
Natural English: “My master’s (program) is difficult but interesting.”

In Greek, unstressed (clitic) possessive pronouns like μου, σου, του, της, μας, σας, τους normally come after the noun:

• το βιβλίο μου – my book
• η μητέρα σου – your mother
• το μεταπτυχιακό μου – my master’s (program)

Putting μου before the noun (μου μεταπτυχιακό) is ungrammatical in standard Greek. The “my” idea is expressed by this post‑positioned clitic, not a separate word before the noun as in English.

Greek normally uses the definite article with possessive pronouns:

• το βιβλίο μου – my book
• η φίλη μου – my (female) friend
• το μεταπτυχιακό μου – my master’s

Leaving out the article (μεταπτυχιακό μου είναι δύσκολο…) is possible only in certain more marked or poetic styles; in everyday standard speech it sounds wrong or at least very odd.

So in Greek the “default” pattern is:
article + noun + possessive = English my/your/his/her + noun.

μεταπτυχιακό comes from:

• μετά – “after”
• πτυχίο – “degree” (usually bachelor’s)

So μεταπτυχιακό means “postgraduate (thing)”. In practice:

• κάνω μεταπτυχιακό – I’m doing a master’s degree
• το μεταπτυχιακό μου – my master’s program / postgraduate degree

In everyday modern Greek, το μεταπτυχιακό almost always refers to a Master’s level program or degree, not a PhD. A PhD is usually διδακτορικό (δίπλωμα).

Yes. Adjectives in Greek agree with the gender, number, and case of the noun they describe.

• μεταπτυχιακό is a neuter singular noun.

• So the adjectives describing it must also be neuter singular:

  • δύσκολος (m.), δύσκολη (f.), δύσκολο (n.)
    → here we use δύσκολο (neuter)
  • ενδιαφέρων (m.), ενδιαφέρουσα (f.), ενδιαφέρον (n.)
    → here we use ενδιαφέρον (neuter)

So:
Το μεταπτυχιακό (neuter) μου είναι δύσκολο (neuter) αλλά ενδιαφέρον (neuter).

They both agree with το μεταπτυχιακό.

Greek works like English here:

• English: My master’s is hard but interesting (not usually is hard but is interesting).
• Greek: Το μεταπτυχιακό μου είναι δύσκολο αλλά ενδιαφέρον.

One είναι links the subject (το μεταπτυχιακό μου) with both adjectives (δύσκολο and ενδιαφέρον) joined by αλλά.

You can say:

• Το μεταπτυχιακό μου είναι δύσκολο αλλά είναι ενδιαφέρον.

It’s grammatically correct, but it sounds more heavy or emphatic, like you’re stressing the contrast strongly:
“It’s hard, but (still, it really) is interesting.”

In neutral speech, the version with a single είναι is more natural.

αλλά is the basic conjunction meaning “but”, introducing a contrast:

• είναι δύσκολο αλλά ενδιαφέρον – it is difficult but interesting

Compared:

• και – “and”, simply adds information with no contrast:
  
  • είναι δύσκολο και ενδιαφέρον – it is difficult and interesting
    (both are true, presented as compatible, not opposed)
• όμως – “however / though / but”; it’s an adverb, not a conjunction. You’d usually put it in a separate clause or in a different position:
  
  • Το μεταπτυχιακό μου είναι δύσκολο. Όμως είναι ενδιαφέρον.
    – My master’s is difficult. However, it is interesting.

In your sentence, αλλά is the natural choice to show a direct contrast in the same clause.

μεταπτυχιακό is stressed on the last syllable:
με‑τα‑πτη‑χια‑ΚΌ → /me-ta-pti-xi-a-ˈko/

Tips:

• πτ = /pt/ (like “pt” in apt but in the middle of the word)
• χ before ι/ε is like the German ch in ich, or the Spanish j in jefe, but softer: /ç/
• ια is two sounds: /i.a/ → “ee‑a”

Syllables: με‑τα‑πτι‑χια‑κό
Try slowly: με‑τα – πτι – χια – κό, then speed up.

Greek adjectives are usually listed in dictionaries with the masculine form, nominative singular:

• ενδιαφέρων (m.)
• ενδιαφέρουσα (f.)
• ενδιαφέρον (n.)

In your sentence, the subject το μεταπτυχιακό is neuter, so you must use the neuter form:

• ενδιαφέρον – interesting (neuter singular)

So:

• ενδιαφέρων καθηγητής – an interesting (male) professor (masc.)
• ενδιαφέρουσα διάλεξη – an interesting lecture (fem.)
• ενδιαφέρον μεταπτυχιακό – an interesting master’s program (neut.)

Make everything agree in neuter plural:

• το μεταπτυχιακό → τα μεταπτυχιακά (the master’s degrees/programs)
• είναι stays the same (it’s used for both singular and plural)
• δύσκολο → δύσκολα (neuter plural)
• ενδιαφέρον → ενδιαφέροντα (neuter plural)

Full sentence:

• Τα μεταπτυχιακά μου είναι δύσκολα αλλά ενδιαφέροντα.
  – My master’s degrees/programs are difficult but interesting.

Yes, that’s grammatical, but the nuance changes.

1. Το μεταπτυχιακό μου είναι δύσκολο αλλά ενδιαφέρον.

   • Neutral statement. You’re just describing it: My master’s is difficult but interesting.

2. Το δύσκολο αλλά ενδιαφέρον μεταπτυχιακό μου…

   • This sounds like you are introducing or specifying “my difficult but interesting master’s program” as a noun phrase, usually followed by something else:
     
     • Το δύσκολο αλλά ενδιαφέρον μεταπτυχιακό μου ξεκινά τον Οκτώβριο.
       – My difficult but interesting master’s program starts in October.

So your original sentence is a full statement with a verb.
The reordered version is a noun phrase with adjectives that typically needs more context or a following verb.