my credentials for my knowledge on the subject, in case it matters:
(okay honestly I just wanted to show off again)
we'll start simple and then move on to more complex differences to help ease your brother's poor misguided soul onto the path of learning
1. zelda has an overworld, isaac takes place entirely inside a dungeon (or multiple dungeons, depending on how you look at it)
2. zelda has puzzles, isaac does not
3. zelda has the same path every time you play, isaac is different every time: rooms, items, bosses, enemies, literally everything in the game is scrambled every time you start a round of isaac
4. zelda only has one playable character, isaac has seven (each with different perks)
5. zelda is not a twinstick shooter like isaac is
6. zelda features standard medieval objects (sword, bow), isaac features the horrific things that lie beneath isaac's home (parasites, aborted fetuses)
7. zelda features standard dungeon enemies (skeletons, bats, mummies), isaac features -- again -- the horrific things that lie beneath isaac's home (headless children, demon doppelgangers, cysts)
8. zelda is won by completing the game once over multiple sittings, isaac is won by completing multiple runs each done in one sitting
9. zelda is about the adventure of a young boy trying to save the world (and a princess) from an evil pig man, isaac is about a small child's demented imagination and inner conflicts; including the strength of his faith and whether he is destined for heaven or hell, the blame for his sister's death, and breaking his mother's heart, all while contemplating Self Delete
any similarities between zelda and isaac are either common game features for the RPG genre (bombs & keys, shops, dungeon levels) or direct references to the zelda series as an homage (blue candle item, "I AM ERROR" room, fires on either side of the shopkeeper in shops)
if your brother still refuses to admit he's wrong after this he's either extremely stubborn, extremely stupid, or extremely trolling you