At its core it controls like Smash TV / Robotron in a randomly generated semi RPG world filled with powerups items and special abilities.
There is not a traditional leveling system in Isaac, instead we used an item system. Every level will have a treasure room, shop, boss and other secret/special rooms that might contain unique items. Special items come in 4 sets, Usable items, Special Weapon upgrades, Passive upgrades and stat boosters. 90% of items in the game stack, so as you progress your character will change into a monstrous powerhouse not only in stats and abilities but also in appearance.
There are currently over 70 special items in Isaac, not counting pickup items.
Aside from these core items, Isaac uses its pickup items as resources in what i call micro puzzles. the core resources in the game are Coins, Bombs, Keys, Hearts, cards and pills each of these pickups can be used in different ways to acquire special items, gain access to shops and hidden areas, kill enemies and also affect gameplay in many other ways.
The game currently has 6 "dungeons" spanning 3 chapters, 6 bosses, 36 enemy types, 4 unlockable characters and tons of dynamic happenings.