The antenna is one of the biggest ones. The Mediatek has a ceramic (patch) which has to be pointed pretty much skyward to get a good signal. The Ublox has the helical ceramic which can be pointed in many orientations.
For a quad/tri/octo/other multi-rotor you can pretty much assume it will be facing the sky all the time so you can get away with the Mediatek.
For an acrobatic/3D helicopter or airplane you may lose signal while inverted or in banked turns/barrel rolls prompting the need for a helical antenna.
General positioning can also necessitate the helical antenna
If you want to try things on your own, rather than go with the provided code, you will discover that the ublox is much better documented. The MediaTek has "custom" firmware which is very poorly documented -- you will need to collect MediaTek documents for devices from several other customers, put the pieces together, and try things.
The MediaTek is physically a little more durable.
The MediaTek can be stubborn sometimes getting a lock (especially if someone is watch) when the signal is weak (indoors) but amazing at maintaining a lock even indoors.
As for losing signal in 3D...maybe. The MediaTek does seem to have some nulls near the horizon (possibly off the corners, I ought to play with that some time to get a better understanding) that may affect you if you spend a lot of time in steep banks. But the inverted thing ... not really. My MediaTeks work just about as good upside down as right side up. I probably ought to play with that some more and quantify the data.
My experiences with the MediaTek have all been very positive, I use an EZ* and have it mounted up on top of the plane, when setting up the plane for flights I lay the GPS down any way up and it still seems to get a lock. The plane / heli' when under "UAV" flight will not do any wild moves, well I hope not! So a 30 - 45 degree bank should in effect still allow a huge part of the sky to be seen. There should be very little in the way of the plane and the open sky a few hundred feet of the ground!
I agree with Ken about the MediaTek seeming more durable, the Ublox seems like it may need a little more looking after.