Do the Virtual Console Pokémon games use the original IV/EV system, or the revised system introduced in gen III?

As per the title, do the VC Red / Blue / Yellow releases use the original system (used for gen I & II), or the modern one (used for gen III onwards)? I suspect it's been updated to use the modern one (possibly with IVs limited to the range of 0..15, and a few other hacks, to mimic the old system), due to compatibility with Bank, but I'd like some clarification on this.

[Note: For the sake of clarity, this question will refer to the old system's IVs as the alternate term determinant values, or DVs for short. Similarly, the old system's EVs will be referred to as the alternate term stat Exp., or SE for short.]

• Original system: In this system, there are four DVs: Attack, Defense, Special, and Speed; DVs are 4-bit nybbles, limiting them to 0..15. The HP DV is determined by the least significant bits of the Attack, Defense, Speed, and Special DVs, in that order; for a pokemon with 4 (0100) Atk, 5 (0101) Def, 7 (0111) Spd, and 6 (0110) Spec, its HP DV would thus be 6 (0110). In gen II, Special Attack and Special Defense both used the Special DV, and gender (female if the Atk DV is less than or equal to the species' gender code, or otherwise male), shininess (shiny if the Atk DV is 2/3/6/7/10/11/14/15, and the other three are 10; due to this, all shinies had an HP DV of either 0 or 8), Hidden Power type & power (too complex to go into here), and Unown's letter (take the middle two bits of the Attack, Defense, Speed, and Special DVs to get a byte, divide the result by 10, and round down to the nearest integer) were determined from DVs, due to personality values not being introduced until the modern system.

  Stat Exp. can be obtained for each of the five stats (HP, Atk, Def, Spec, Spd), to a maximum of 65,535; using the formula sqrt(SE) / 4, where sqrt(SE) (the square root of the Pokémon's SE) is rounded up to the nearest integer (with a cap of 255, placing the value in the same range as modern system EVs), and the end result after division is rounded down, this results in up to +63 points gained per stat from SE. When a pokemon is defeated, its base stats are added to the victor's SE; vitamins add 2560 SE to their stat, up to a maximum of 25,600. SE can still be obtained at Lv.100; due to the final stat values not being stored when a Pokémon is put in a box, the box trick can be used to force recalculation of a Lv.100 Pokémon's stats. [In gen II, Special Attack and Special Defense share the same Special SE, SE obtained is determined from the defeated Pokémon's Special Attack, and Pokérus was introduced.]

• Modern system: In this system, there are 6 IVs: HP, Attack, Defense, Special Attack, Special Defense, and Speed; IVs are 5 bits long, limiting them to 0..31. Gender, shininess, and Unown's letter, among other things, are determined by the Pokémon's personality value, being independent of the IVs; gen IV later split Unown's letter off into a separate value. Hidden Power type & power are still calculated from IVs; gen VI locked its power at 60, without affecting type calculations (due to this, its type cannot be Fairy).

  EVs were significantly simplified, compared to the old system. Each Pokémon can have a maximum of 510 EVs distributed among its stats, with a maximum of 255 in a single stat (reduced to 252 in gen VI, to prevent the player from inadvertently wasting 3 EVs); this means that a Pokémon can only max out 2 of its stats, compared to all 5 with the original system. Defeated Pokémon add 1-3 EVs to a single stat. Evs still add up to +63 points per stat, albeit with the much simpler formula of EV / 4, rounded down. Vitamins add 10 EVs to their stat, up to a maximum of 100, and can't push the Pokémon's total EVs over 510; Zinc was introduced as the Special Defense vitamin, and Emerald introduced the EV-decreasing berries. Additional EV manipulation items were released in multiple generations. In gen III & IV, EVs are only gained when Exp. is gained, preventing EV gain at Lv.100, and stats are recalculated upon level up (Deoxys is an exception; its stats are recalculated after every battle); in gen IV, stat recalculation can be forced for Pokémon with alternate forms that change their stats, by changing their form. In gen V, this flaw is fixed; EVs can be gained even at Lv.100, and stats are recalculated after every battle.

Considering these significant differences between the original and modern systems, it would be impossible to directly port a Pokémon from a game using the original system into one using the modern system, or vice versa. Considering this, and that the VC releases are compatible with Bank, the question is thus:

Do the VC releases use the modern IV/EV system internally (possibly with restrictions imposed to emulate the original system), or do they use the original system (but convert Pokémon to the modern system upon transfer to Bank)?

tl;dr: IVs and EVs are the same as they were originally while playing RBY. However, these values change when you transfer Pokémon to the Pokémon Bank. At this point, IVs will be semi-randomly generated upon transferral and EVs are simply set to 0.

The 3DS ports of Red/Blue/Yellow were kept virtually the same as the originals, even including the same glitches (like the Mew glitch on Nugget Bridge). For reference, here is a list of differences between the 3DS Virtual Console versions and the originals.

This means the old EV/IV system was also maintained. However, this does not translate to the current system, as you've mentioned in the question.

According to this article based on datamines of the games, it doesn't have a system similar to the current one at all. In fact, it seems that Pokémon will simply be assigned EVs and IVs when transferred to Pokémon Bank.

Individual Values (IVs) are determined randomly. However, at least three stats will have a perfect value of 31. That means that every transferred Pokémon from RBY will have three good stats at least! The exception is Mew, who gets at least five perfect IVs instead.

Effort Values (EVs) are set to zero.

Similarly, Natures will be generated upon transferral, though these are based upon EXP earned.

Nature is an interesting aspect. Bank determines what the new Nature is based on the gained EXP of the Pokémon:

Nature = EXP % 25

% represents the ‘modulo’ operator, and gives you the remainder when dividing by the number following it. If EXP was, say “1001”, the equation becomes 1001 % 25 = 1, as dividing 1001 by 25 gives you a remainder of 1.

Each number corresponds to a Nature, which is listed below (assuming the same system is maintained). If you’re determined to get a good nature for your RBY Pokémon, you can give it some EXP to do just that!

As for Abilities, most Pokémon appear to be given their Hidden Abilities, with the exceptions being those that don't have Hidden Abilities:

Almost every Pokémon from RBY will gain its Hidden Ability. There are three exceptions; Mew, the Weezing line, and the Gengar line. This is because these Pokémon have no Hidden Ability.

This means that Machop will not have the No Guard Ability when transferred. No Guard Fissure Machamp can’t exist!