Flap thickness (both in predicting actual thickness, as well as in minimizing topographic variability of flap thickness) is a major plus when using newer Femtosecond lasers.  

Article Three-dimensional LASIK flap thickness variability: Topograp...

Excellent question. I had an experience with both. Yes, the flaps with femto are more consistent in their shape and have the same thickness all the way, but honestly there is no difference in patient satisfaction between femto and microkeratome.

I did LASIK to my own eyes, I could choose between the femto and microkeratome, and I've chosen the second one. It takes less time to create a flap, the vacuum on the sclera is also shorter and I believe more the hands of the surgeon than the machine. Furthermore, femto is more expensive per surgery. 

I would start reversely:  yes, microkeratome costs less.  But the question is in 'superior clinical results'.  In the majority of cases, there may be no real difference between a 140 μm flap that was meant to be 110 μm deep, not a 8.20 mm diameter flap that was meant to be 8..00 mm.  The accuracy of the excimer laser ablation, both in it's centration as well as delivering the proper ablation profile (factor in cyclorotation in customized treatments) may be far more important.  The close-call cases, though, may be those that will give you the answer.  Check this article 

Article Unilateral Corneal Ectasia after Bilateral LASIK: The Thick ...

From a vitreoretinal stand point, there is no stress induced at the vitreous base by femtosecond laser in creating the LASIK flaps, whereas any mechanical microkeratome has the potential of inducing vitreoretinal stress.  Although, there is no unequivocal proof in linking LASIK with vitreoretinal complications (e.g. breaks and RD), there are multiple anecdotal case series in the literature showing such complications following LASIK (acute vitreoretinal stress at the vitreous base induced by the mechanical microkeratome is a potential mechanism for such complications).. 

See my following published references:

Chan CK, Arévalo JF, Akbatur HH, Sengün A, Yoon YH, Lee GJ, Tarasewicz DG, Lin SG.  Characteristics of sixty myopic eyes with pre-laser in situ keratomileusis retinal examination and post-laser in situ keratomileusis retinal lesions.  Retina 2004; 24:706-713.

Chan CK, Tarasewicz DG, Lin SG. Relation of pre-LASIK and post-LASIK retinal lesions and retinal examination for LASIK eyes. Br J Ophthalmol 2005; 89: 299-301.

Jóhannes - without question - femtosecond flaps have a number of advantages that provide significant benefits to patients. The most important is that femto flaps fit back into place more precisely, as the bed is created to allow the flap to settle back in place - resulting in less microstriae.  In contrast - with a manual microkeratome, the flap lays back, but can shift and not settle back as easily into position.  Yes - grossly - microkeratome flaps look like they are back in position.  But - when you remove the epithelium for enhancements, you are more likely to see microstriae with microkeratome flaps as compared to femto flaps (in my experience).  This suggests that the flaps just fit better back into place.

   The second major issue is that the femto flap is the same thickness throughout, while microkeratome flaps have a meniscus shape, meaning that they are thicker paracentrally as compared to centrally.  So - this leads to the cornea being less biomechanically stable.  Since microkeratomes go deeper in certain areas, it also results in deeper impact on corneal nerves, with he potential for a little more dry eye.  However - that is theoretical.

    Obviously - in experienced hands - the results with microkeratomes can be very good.  However, femto allows less experienced surgeons, or lower volume surgeons, to provide consistent results.  

    I hope this helps.  I am always happy to answer or respond to any questions regarding my thoughts on this manner.  Best regards.  Bill

I agree with the theoretical advantages mentioned by Dr Trattler. But with new generation microkeratomes those advantages are more theoretical than real. I do a large amount of eyes with both femto and microkeratome and there is no significant clinical difference. If I had to do a treatment to myself I would use microkeratome

There is a lot of subjectivity when comparing the femtosecond laser versus the microkeratome. One major difference is that with the laser  the flap diameter and thickness, the position of the hinge, and the angle of the edge of the flap are easily controlled. The later allows for a positive lock in place allowing the flap to withstand many Gs of acceleration or deceleration. The US air force allow its pilots to have Lasik surgery but only all laser Lasik.