Hello!
I presume you mean the 3 step processes?
Mothers all the way! Heres why:
IMO the Step 1 is pretty much the same in both of the ranges, no difference there.
Step 2, the Mothers Sealer and Glaze (does not seal the paintwork) fills more imperfections then Meguiars Deep Crystal Polish (no mechanical abbrasives or chemical abrassives). Mothers also gives a deeper, richer look. The Meguiars stuff can dry fast and be a PIA to remove. Both are apply a panel at a time and wipe off products.
Step 3 is where the Mothers out right wins, there wax is much nicer looking and longer lasting then Megs Deep Crystal Wax. If you get the tin instead of the liquid it will last ALOT longer too. In the UK i can manage about 9 weeks of good looking protection from the Mothers wax.
Both systems are effective but fairly old and in need of an overhaul. But if thats all you can choose go with the Mothers.
Geoff