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Dr. Mario is considered to be a "clone" of Mario, since he is a slower, yet stronger version of Mario.
This blog is a comparison between the default, unaltered versions of Mario (SSBWU/3DS) and Dr. Mario (SSBWU/3DS).

Comparison: Mario/Dr. Mario (3DS)

Attacking: Zelda

Attack Mario Dr. Mario Winner
Up Throw7%7.5%Dr. Mario
Forward Throw  8%8.5%Dr. Mario
Down Throw5%5.5%Dr. Mario
Back Throw11%12%Dr. Mario
A2.5%2.5%X
Grapple A3%3.5%Dr. Mario
AAA8%8.5%Dr. Mario
Up-tilt6.25%7%Dr. Mario
Side-tilt7%7.5%Dr. Mario
Down-tilt5%, 7%(TCH)5.5%, 7.5%(TCH)Dr. Mario
Up Smash14%–19.5%15.5%–21.5%Dr. Mario
Side Smash14%–19.5%(TooCl) 17%–23.5%  15.5%–21.5%, 19%–26.5%(TCH)  Dr. Mario
Down Smash10.25%–14%, 12%–16%(Rear)11%–15.5%, 13.5%–18.5%(Rear)Dr. Mario
Air5%(BH) 8%5.5%, 8.5%(PH)Dr. Mario
Up Air7%7.5%Dr. Mario
Forward Air12%(BH) 14%10%(BH) 15.5%Mario/Dr. Mario
Down Air10%(FC)12.5%(FC)Dr. Mario
Back Air7%(BH) 10%7.5%(BH) 13%Dr. Mario
B4%(Far) 5%4.33%(Far) 5.5%Dr. Mario
Up B12%(FC)6%(Far) 13.33%Dr. Mario
Side B7%7.5%Dr. Mario
Down BN/A8.5%(FC)Dr. Mario DiffAtt
Final Smash~10%(Far) ~47%(TCH)~16%(Far) ~50%(TCH)Dr. Mario

Less Nimble? Yes! Stronger? Yes! Other differences include Dr. Mario's Side Smash, Neutral Aerial, Neutral Special, and Final Smash.

Mario's fiery Side Smash is most effective if he isn't touching the opponent, while Dr. Mario's electrical Side Smash is most effective if he is touching the opponent. They are opposites.
Dr. Mario does not throw Fireballs, he throws Megavitamins. These huge pills bounce high and are more damaging than fireballs.
For a perfect hit, Dr. Mario's Neutral Aerial must hit the opponent during the animation, but not instantly; the hit must be delayed. Offensively, this can be accomplished by initiating his aerial, missing, floating him mid-animation toward the opponent, then landing the delayed hit before the animation ends.
Mario is the opposite, his aerial is strongest if it lands upon activation, and weakened by delay.
Dr. Mario's Final Smash is only slightly more effective than Mario's; it deals more damage with a longer range.

Specials

Below is a comparison between their unaltered Special Attacks.

Mario Game Description Dr. Mario Game Description
FireballThrows a fireball that bounces along the ground.MegavitaminsThrow a vitamin capsule that bounces off the ground
CapeWhips out a cape to spin opponents around and reflect projectiles.Super SheetA sheet that reflects projectiles. Has a short reach but a wide vertical range.
Super Jump PunchA rising punch that hits repeatedly.Super Jump Punch This rising punch may have no coins involved, but it's extra powerful at the start of the jump.
F.L.U.D.D.Blasts opponents with water. It can be charged and aimed at an angle.Dr. TornadoSpins repeatedly. You can move sideways while spinning and press the button repeatedly to rise.

Key

Acronym Meaning Specifics
TCH Touching Used when player is touching the opponent.
TooCl Too Close Used when the player is too close for the attack to do full damage.
BH Bad Hit Used when the attack is performed in a manner that decreases damage.
PH Perfect Hit Used when the attack is performed in a manner that increases damage.
May lose comparison due to difficulty.
FC Full Contact Used when the attack lands every hit.
DiffAtt Different Attack Used when the compared attacks are not similar.
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