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How Many Pokémon Can You Get with Only Pokémon Emerald?

Emerald has two separate Pokédexes to complete: the Hoenn Pokédex and the National Pokédex. The Hoenn Pokédex contains 200 Pokémon (202 counting Jirachi and Deoxys), which includes every Pokémon introduced in Ruby, Sapphire, and Emerald, while the National Pokédex consists of the Hoenn Pokédex plus the other Pokémon introduced in Red, Green, Blue, & Yellow and Gold, Silver, and Crystal (Pokémon 1-251). All Pokémon from the Hoenn Pokédex, except for the event-exclusive Jirachi and Deoxys, are available between Ruby, Sapphire, and Emerald. Only a select few Pokémon from the National Pokédex are available in Emerald. This page will cover both the Hoenn and National Pokédexes.

The number of Hoenn Pokédex Pokémon that are available without trading is 179. The list of Pokémon you cannot get without trading, which equals 23 species, is as follows:

Two Starters (6) - 6 total
As you can only select one starter Pokémon, the other two starters, and their evolutions, are unavailable; this totals 6 Pokémon.
Trade Evolutions (6) - 12 total
Golem, Machamp, Alakazam, Kingdra, Huntail, and Gorebyss evolve by trade. Without the ability to trade, they are unobtainable.
Version Exclusives (7) - 19 total
The following Pokémon cannot be obtained without the use of glitches, trading, or events: Surskit, Masquerain, Meditite, Medicham, Roselia, Zangoose, and Lunatone.
One of Latios and Latias (1) - 20 total
The player must choose between Latios and Latias after defeating the Elite Four, leaving the other one inaccessible.
Moon Stone Evolutions (1) - 21 total
Emerald players can only get one Moon Stone, but two Pokémon require it: Delcatty and Wigglytuff. One of these Pokémon is therefore unobtainable.
Mythical/Event (2) - 23 total
Outside of glitches, Jirachi and Deoxys were only obtainable via events that are no longer active, or in Jirachi's case via the Colosseum Bonus Disc (which requires trading).

The number of National Pokédex Pokémon available without trading is 212. The list of available National Pokédex Pokémon that aren't in the Hoenn Pokédex is as follows:
Meowth, Persian, Ditto, Hoothoot, Noctowl, Ledyba, Ledian, Spinarak, Ariados, Mareep, Flaaffy, Ampharos, Sudowoodo, Aipom, Sunkern, Sunflora, Wooper, Quagsire, Pineco, Forretress, Gligar, Snubbull, Granbull, Shuckle, Teddiursa, Ursaring, Remoraid, Octillery, Houndour, Houndoom, Stantler, Smeargle, and Miltank

The Professor Oak challenge guide for Emerald, which covers the National Pokédex, can be found here, although I've made a shorter list of encounters below in case anything happens to the external guide.

Professor Oak Challenge Notes

Pre-Badge 1 (Roxanne) - 39 Total Pokémon

Badge 1 through Badge 2 (Wattson) - 66 Total Pokémon

Badge 2 through Badge 3 (Flannery) - 90 Total Pokémon

Badge 3 through Badge 5 (Norman) - 101 Total Pokémon

Badges 5 through 6 (Tate & Liza) - 156 Total Pokémon

Badges 6 through 7 (Wallace) - 167 Total Pokémon

Badges 7 through 8 (Winona) - 171 Total Pokémon

Post-Elite Four - 178 Total Pokémon

Post-Elite Four - National Pokédex - 212 Total Pokémon

All National Pokédex Pokémon are only available after defeating the Elite Four.