Non-Legendary Tier List (second beta)
New trainers, experienced trainers starting new accounts or returning from a long break, casual solo trainers and rural trainers may have limited access to many legendaries and rare candy. Besides legendary species, regional species and those that are only viable with legacy moves are excluded for similar reasons. Defensive ability is taken into consideration (since defence does matter in many areas and gym coins are valuable), but generally not as much as offensive ability.
Tier 1
Machamp (Counter + Dynamic Punch): Most crucial gym attacker due to dominance of Normal-types, with Lapras and Steelix also common, main counter in Tyranitar, Absol and Regi-trio raids; can be acquired through raids.
Dragonite (Dragon Tail + Outrage): Top generalist gym attacker, good gym defender, counter to many Dragon-type legendaries; Hurricane is useful for Machamp solos.
Blissey (Zen Headbutt + Dazzling Gleam): Best gym defender and main coin source.
Tyranitar (Bite + Crunch): Crucial to Alakazam, Gengar and Jynx solo teams, top counter to many Psychic-type legendaries including Mewtwo; Stone Edge is useful against Flying-type legendaries; can be acquired through raids.
Tier 1.5
Gardevoir (Confusion + Dazzling Gleam): Great for Machamp solo teams, fantastic gym defender, counter to many Dragon-type legendaries and gym defenders.
Gyarados (Waterfall + Hydro Pump): Good generalist gym attacker, good gym defender, counter to some Tier 4 raids and future legendaries.
Hariyama (Counter + Dynamic Punch): Similar roles to Machamp, with lower DPS but higher TDO.
Tier 2
Alakazam (Confusion + Future Sight): Crucial to Machamp and Gengar solo teams; Psycho Cut is good for dodging and Focus Blast can attack Normal-type tanks in gyms.
Flareon (Fire Spin + Overheat): Great for Jynx solo teams, relevant gym attacker; easy to acquire.
Salamence (Dragon Tail + Draco Meteor): Slightly worse Dragonite due to less flexible moveset.
Tier 2.5
Espeon (Confusion + Future Sight): Slightly worse Alakazam due to less flexible moveset; easy to acquire.
Gengar (Hex + Shadow Ball): Crucial for Alakazam and Gengar solo teams; even stronger with legacy move Shadow Claw and has other niche roles with Sludge Bomb.
Golem (Rock Throw + Stone Edge): Top counter to many Flying-type legendaries, niche gym attacker; may be eclipsed by Rhyperior in Gen IV.
Exeggutor (Bullet Seed + Solar Beam): Relevant gym attacker, crucial for Omastar solo teams, can contribute to Machamp solo teams with Extrasensory + Psychic; easy to acquire and even stronger with legacy move Confusion.
Tier 3
Snorlax (Zen Headbutt + Heavy Slam): Great gym defender, will earn many coins; niche gym attacker.
Chansey (Zen Headbutt + Dazzling Gleam): Great gym defender, will earn many coins.
Rhydon (Mud Slap + Earthquake): Niche gym attacker, counter to some Electric-type legendaries, Regirock and Registeel; has great evolution in Gen IV.
Metagross (Bullet Punch + Flash Cannon): Relevant gym attacker, great for Jynx solo teams, can contribute to Machamp and Gengar solo teams with Zen Headbutt + Psychic.
Tier 3.5
Vaporeon (Water Gun + Hydro Pump): Relevant gym attacker, counter to some tier 4 raids and future legendaries; easy to acquire.
Jolteon (Thunder Shock + Thunderbolt): Relevant gym attacker; easy to acquire.
Sceptile (Bullet Seed + Leaf Blade): Relevant gym attacker and great for Omastar solo teams; Fury Cutter is better if adversary is not weak to Grass-type attacks.
Tier 4
Charizard (Fire Spin + Overheat): Has lower DPS than Flareon but doubly resistant to Bug-type and Grass-type attacks; better than Flareon with legacy move Blast Burn.
Jynx (Frost Breath + Avalanche): Niche gym attacker, counter to many Dragon-type legendaries; faces stiff competition from Lapras/Walrein and will be eclipsed by Mamoswine in Gen IV.
Houndoom (Snarl + Foul Play): Inferior to Tyranitar but can contribute to Alakazam, Gengar and Jynx solo teams.
Scizor (Fury Cutter + X-Scissor): Niche gym attacker, counter to many Psychic-type legendaries; can be slightly worse Metagross with Bullet Punch + Iron Head.
Answers
Gyarados has 12.2% higher DPS but 8.2% lower TDO than Vaporeon. For comparison, Kyogre has 11.9% higher DPS than Gyarados and 24.7% higher TDO than Vaporeon.
Keen to duo Houndoom or Golem in rain? Gyarados is viable at level 30 but Vaporeon is only viable at level 40. For Rhydon duos, level 35 Gyarados is viable in neutral weather while level 35 Vaporeon will only work in rain.
Predictable moves also hamstring Vaporeon on gym defence. Water Gun barely tickles Dragonite and Exeggutor (which is easy to acquire even for rural players), while Gyarados walls Machamp. In rural areas with limited access to legendaries, Gyarados is an absolute beast, as its best counter, Jolteon, is quite glassy.
The only Electric-types "better" than Jolteon are legendaries, but what optimal niches are there for Jolteon? Gyarados and perhaps Milotic. Jolteon is otherwise a backup option, to Exeggutor against Water-types and to Golem (or Jynx) against Flying-types (ignoring Omastar because only legacy moves are viable).
In conclusion, Jolteon may belong in tier 2.5 or 3, while Vaporeon deserves to be in tier 3 or 3.5.
Placement of Snorlax, Blissey, and Chansey dependant on the importance of gym defense for an individual. In crowded big cities, without one of these three, you're unlikely to get many coins unless you're glomming onto someone else's BlissChanLaxes. Possibly add Aggron as a second tier defender, but bumped down because of its weaknesses.
Gyarados in gyms? Jolteon shreds it. In general, good defenders are about having few weaknesses, because intelligent attackers will always attack that weakness. Gyarados (electric), Tyranitar (fight), and to a lesser extent, Dragonite (ice), are not good defenders because of that.
