My recommendations are as follows. Your mileage may vary.
The Magnifier with the 4 MOA has a big ass reticle. I havent used it with the 2 MOA, but that would be my choice for a magnified Aimpoint setup. You can always crank the scope so it blooms and seems bigger. The reticle won't get smaller, however.
The ONLY reason to buy the M3 over the ML3 is for nightvision. If you might aquire nightvision, thats the one to have. If its out of the picture, might as well get the ML3.
As for zeroing.....the 100 yard zero sucks. Past 100 yards it drops like a rock. If you zero at 50m you will be on at 200 and vice versa. Note that 50/200 is in metric. This makes for something like 8" low at 300 and 20" low at 400, off the top of my head.
For best accuracy, turn the reticle WAY down. This makes it seem a touch smaller and much more regular. Don't bother trying to shoot at whats under the reticle, shoot at whats around it. A dot on the target slightly bigger than the size your reticle appears at that distance is perfect. Center the dot and squeeze the trigger.