Modern Emerald vs Vanilla Emerald: Every Change That Matters

Modern Emerald is, in the author's words, "a modernization of the original Pokémon Emerald game" — a 2.0 update rather than a difficulty hack. It is a Gen 3 game at its core, and most of what makes it modern is chosen at new game, not baked in. The same ROM can give you a near-vanilla run or a heavily reworked one.

The short answer

If you want vanilla Emerald with quality-of-life additions, pick the Classic preset and Original encounters. If you want the modern experience, pick Modern — it enables the physical/special split, the type chart rebalance, Fairy, modern typings and the new encounter tables. Everything below can also be set individually.

Encounters

Three encounter modes at new game: Original (genuine vanilla tables), New (the hack's own tables across the whole game) and Postgame (vanilla until you beat the league, new tables after).
The game ships 436 species in its data, including later-generation additions; the documentation describes "423 Pokémon" for the roster it advertises. Both numbers appear in the hack's own materials — the data file count is the one the site can verify.
Route-by-route, most areas keep their vanilla species and gain a few. Water routes change the most. Every route where the New tables differ is compared on the encounters-by-route page.

Difficulty (optional, chosen at new game)

Easy, Normal and Hard, plus a separate Level caps option with Normal caps and Hard caps variants.
Easy scales trainer and wild Pokémon down — roughly 10 levels below vanilla, with more of a gap the more badges you have — and gives +30% EXP. There are no Battle Frontier restrictions on Easy.
Normal is vanilla, with rematches and the small shared changes.
Hard lowers EXP gain, scales levels up, and adds the Frontier restrictions and legendary stat changes below.
Hard mode is where most of the difficulty lives: EXP gain cut 40%, damage taken multiplied by 1.10–1.25 as you earn badges, forced Set battle style, a four-item limit in trainer battles, a Battle Frontier legendary ban, boosted legendary stats and lowered catch rates, and per-ace changes — Norman's Slaking loses Truant, Juan's Kingdra and Wallace's Whiscash set rain.
The badge-by-badge cap numbers for both cap variants, in both modes, are on the level caps page; they are read straight from the hack's src/caps.c.

Battle mechanics (optional)

Physical/Special split — Gen 4-style, toggleable.
Type chart rebalance — Improved (eight matchup changes) or Gen VI+ (those eight plus Steel no longer resisting Ghost and Dark). The site's type chart tool shows the Gen VI table; the guide lists the ten entries the options change.
Fairy type — optional, and it retypes Pokémon rather than only adding the type to the chart.
Modern typings, better stats and extra legendary abilities are separate toggles. Against the vanilla data this comes to 37 retypings, 62 stat buffs, 23 ability changes and 14 new moves — the pokemon-changes and move-changes pages list them.
HM moves can be used without teaching them if you hold the HM and have the badge, and HM slots are Nuzlocke-safe.

Story and world

Name your rival; pick an outfit from the outfit box.
Gym rematches trigger 50% of the time after 10 wild or 5 trainer battles won.
Elite Four and Wallace rematches, plus a Steven rematch whose team runs level 85–88.
New areas gated behind the Sealed Chamber puzzle, including an extra Route 110 and Route 132 area, the Draco Chamber and the Cave of Shock.
Legendary and mythic encounters are all reachable in-game — Mew, Deoxys, Jirachi, Mewtwo, Ho-Oh and Lugia are behind Battle Frontier tickets, and Celebi and Regigigas need specific parties. All of them are listed on the legendary page.

Quality of life

Double-speed battles, following Pokémon, no-save-scum, faster text, item drops from wild Pokémon, an in-game Wonder Trade, a Pokémon stats page, reusable TMs (optional), fast egg hatching, nickname changes, and an IV/EV editor on the summary screen from the Oldale Town NPC.
A Real Time Clock option for emulators without one, so daily and night-time events still work.

What stays the same

The map, the story beats, the gym order, the Hoenn Pokédex progression and the battle engine are Emerald's. Item locations are largely vanilla too — only the changes and additions are listed on the item locations page.

All figures cross-checked against the extracted game data (vanilla_diff.json, level_caps.json, tmhm_locations.json); option names and behaviour from the hack's official documentation and its open-source repository.