First, decide whether the Mega we already have for that Pokemon is the 'Y' (progressing from and accentuating things set up in the base form) or the 'X' (radical thematic shift, more 'unnatural' progression). Design your new Mega accordingly.

Try to give the new Mega a different (not flatly better or worse) niche than the one we already have.
If you feel like it, give an example set.
Have fun!

I'll start
Mega Sceptile Y
>Type: Grass/Dark
>Design: Lean, colour scheme becomes darker, tail becomes thinner, blades are now continuously extended and glowing green.
>Ability: Super Luck
>HP: 70
>Atk: 85 > 145 (+60)
>65 > 75 (+10)
>105 > 110 (+5)
>85
>120 > 145 (+25)

Rationale: When Gen 4 hit, Night Slash and Sceptile's signature Leaf Blade became Physical moves, defeating the purpose of its higher Special Attack.
This Mega aims to give Sceptile back its blades. Super Luck gives the dual STAB of Leaf Blade and Night Slash 50% chance of critical hit.

Example Set:
Adamant or Jolly, 252 Atk/Speed
>Leaf Blade
>Night Slash
>Earthquake
>Thunderpunch
You also have setup options with Focus Energy or Swords Dance, but remember your frailty.

Is it too OP?