It's really a matter of personal preference as both can work equally well for anybody who knows what he's doing. I can and do use either just fine, but it is nice to have most of your stuff using one system or the other so once people find a preference they tend to try and stick to it with most new purchase. My preference is Mil/Mil for a few reasons.
The first is availability. While more and more MOA scopes have been showing up recently, which is a good thing, Mil scopes still outnumber them probably 5 or 10 to one. If you must have MOA you're eliminating a bunch of fine scopes from your list of possible choices. Spotting scopes as well—a spotter with a good reticle is a wonderful tool to have while spotting for somebody—especially at really long ranges.
Another is click value. I find .1 Mil or 1/3 MOA clicks about the right size for me as a good compromise between how fine the divisions are and speed and amount of travel per turn of the knob. Of course there are ½, 1/8th even 1 MOA scopes as well as .2 Mil, .05 Mil, so it isn't always the case, but most of the scopes I look at tend to be either .1 Mil or ¼ MOA.
Finally, I find the numbers are easier to deal with. 7.5 instead of 25.75 or 25 ¾ is simply easier for me to read off a PDA, enter in drop chart, read off a drop chart, call out to my buddy, etc. With my 300 RUM drops are a simple two digit number out to 1300-1400 or so depending upon load so drop charts are nice and neat. It's not a big thing, just something that makes things nicer to deal with.
In all my Engineering jobs we've always used inches (yes, we still use inches) but with decimals. Nobody measures things in fractions. If you give the average guy a ruler where the inches are broken up into tenths and hundreths, after using it only a couple times that's the one he'll reach for any time he needs to measure something over one with halves, quarters, eighths, sixteenths, thirty-seconds, sixty-fourths, etc.
And no, there is nothing "metric" about Mils nor do you need to "convert to the metric system" to use such a scope as some will say. They work just fine with yards. This seems to be a misconception most commonly held by those with little long range experience who still think of elevation and windage in "inches" and "clicks."
If you do, you should stop doing that.
If you think in angular units, be they MOA or Mils you will save yourself a lot of thinking/calculating/headscratching. It's different for competition target shooters who shoot at the exact same target at the exact same distance all the time, especially when the rings of the target are in inches or MOA sized. But for all different sizes of animals at all different ranges, all different sizes of steel targets at all different ranges, getting your dope in inches then trying to figure out what that means in relation to
this target at
this range is a nightmare.
If you get your dope in angular units, correct for it with either the turrets or reticle, it works for any sized target at any range. You don't spend a single millisecond trying to think/converting/do math so it's much faster and there is zero chance of a math/conversion error causing a miss. Once people learn to do that and find they no longer use "inches" for anything anymore, they usually become less emotionally attached to MOA's and find they do just fine with either MOA or Mil.