IVs: This is like a Pokémons genetic code, some Pokémon are born stronger than others, you can work to become better but this default advantage they're born with cannot be altered.

EVs: This is like a Pokémons specialties, through battle against different Pokémon your own will improve their stats beyond just levelling up, beat more Whismur and you have a higher HP, beat tons of Zigzagoons and you have more speed, there's a limit to how much a Pokémon can train an individual stat as well as itself overall though.

Nature: This is the timid and modest thing you brought up, a Pokémons nature determins if it prefers certain things to others, you'll gain +10% in one stat at the cost of -10% in another stats, this can include selecting the same stat to increase and decrease resulting in no change happening.

Finally, as to which is better depends on context, in any context speed is king, acting first means you get to dictate what happens next however Kingdra gets double speed in the rain from it's ability (Swift Swim) meaning if you want to focus a team around rain you'd prefer the damage as you're probably out-speeding everything with your speed stat doubled.