Disclaimer, I'm probably the worst player in this thread, so I feel like I'm in a stage where I can't really condition people to do anything but bait me over and over with really scrubby stuff because of horrible reads. I'm getting bodied constantly and I'm not sure how much of it is the character's flaws since this is the first MK I'm taking semi-seriously (coming from this as a slightly above average SF player).
I can open with F44 because no one expects the low hit, but then I feel like I have nothing to follow up on. Any attempt at F343 gets stomped, even at wakeup. Same with jump-ins. Erron Blacks and Takedas in particular are just outzoning me to death and I feel like I have no options from full screen except for a desperation TK. Executing rolls on a 360 pad is also hell on earth. I'm whiffing that way too much. Maybe I'm underutilizing sais?
Which variation are you using at the moment?
Mileena's playstyle stays pretty consistent between Piercing and Ravenous (Ethereal needs a buff) so it doesn't make that much of a difference, but Piercings improved Sai basic strings and access to a low projectile can give you an option or two more if you're struggling to get in and make use of Ravenous's damage.
If you're getting zoned you can use Sai's to try and give yourself a little freedom to get closer, full-screen is pretty rough though. From a middle distance you can roll-punish a decent amount of stuff but be careful to not be too predictable with it because you'll be punished hard on whiff.
Ex roll also has armor so bare that in mind when you have meter. Ex TK combos on hit so if you can try and hold it for a punish and get some damage in it can make your opponent respect your meter at mid-full screen which might relieve some pressure.
F343 and F344 are big damage openers, but hardly reliable. I'd recommend staying away from them unless you've got a huge punish opportunity or you're certain that you've got your opponent blocking low against you. They're basically the "I can do anything I want right now because I've got a free hit" strings.
Speaking of strings, don't be concerned if you're not getting huge damage from low hits. If you're getting low hits in consistently (even if they don't lead to big damage) then your opponent is going to start predicting the low hits at some point.
Once they are blocking low you can cancel your string into a Ex BR for an overhead mid-string or throw out F3 if you're feeling lucky, if you're in Ravenous you can cancel pretty much any string into the Low Pounce chain grab too (having a low throw is awesome against habitual low-blocking opponents).
Oh and a quick note, if you aren't already, try using the following follow ups for stray low hits. It's basically my go-to small combo for stray hits.
(Hit), BR, B3, TK, AS, F12, Low Pounce (Ravenous)
(Hit), BR, B3, TK, AS, B12, 1+3, DD2 (Piercing)
