One little tip would be to take advantage of Reptiles weird hitbox.
When Mileena executes a regular telekick cancelled into sai on any character, the kick will make contact but the sai will wiff overhead leaving you to be punished. However, against Reptile you can abuse the regular telekick a little becuase (for some reason) the sai will always hit him in the face on stand block and you will be granted advantage. If he crouch blocks, the sai will not hit but his options are limited, Reptile does not punish Mileenas telekicks very well.
You also need to heavily zone with projectiles from full screen. Use your ground sai and instant air sai (at face level) heavily to nullify the green balls and dash. You can also try to tone down the zoning at some point to bait a green ball. Due to the slow start-up on this move, you can easily telekick on reaction and be granted +31 on hit and a free jump in + pressure.
Don't try to fight him around jump distance and go in for D4's because Reptile will dash you to oblivion. Also, naked rolls are not recommended; if blocked, this is Reptiles opportunity to hit you with a higher damage combo and set-up a pressure game with an EN Slow Ball combo ender. All of a sudden he will be in on offense and you will have to take or counter whatever he dishes out.
This is a great match-up that can easily go either way. It all comes down to the player and their use / abuse of mindgames.
