You can have excellent outcomes with either. Intralase costs more because a second and very costly Yag laser is needed, but it allows a lower-vacuum force on the globe during flap cutting, which interferes less with perfusion. The time on application is short with the higher-force microkeratome fixation ring and it has not been thought to be significant as to its effect on ocular perfusion, but nonetheless, the difference is there. Probably more significant is the ability to create very uniform and thinner flaps with the Intralase (femtosecond YAG laser--IR wavelength) than with a microkeratome which allows for a thicker stromal bed from which to perform the stromal ablation (done with the excimer laser, UV wavelength).
In cases where the planned correction requires ablations that approach the limits of requirements for thickness of remaining corneal stroma (something you need to retain structural stability of the cornea and to avoid irregular astigmatism and poor post-operative vision), many experienced refractive surgeons choose not to cut a corneal flap at all and to ablate from the front surface as in PRK. This requires consideration of particular ablation patterns to use, choice of combinatons of ablation patterns and even selection of one make of excimer laser over another for that particular case depending on the laser's particular beam profile and performance at the treatment margins, considerations beyond this discussion.)
The flap design of the Intralase allows for something of a beveled or vertical "ship's hatch door fit" which theoretically limits any tendency to have the cut flap wander side to side post-op, whereas a shelved cut from a microkeratome does not afford this incisional architecture.
That all said, excellent outcomes can be had with either. 99% of the quality of laser refractive surgery outcomes are determined before anyone sets foot in the laser room.
