If you are earning 150K+ a year, you might want to consider using both FF programs (i.e. earning AE Elite and then going for MP top flight status). This way you would get upgrade certs for both.

Also, if you fly a lot in the US, AC-E will get you into lounges for free, but I believe UA and US elite members have to pay a fee to get into the lounges (not that you would want to pay to enter a RCC).

I'm not sure, but I think that the UA upgrade certs are only provided for miles flown on UA metal, so you would likely want to credit all UA flights to MP. You would also want to credit your AC flights to AE in case you chose the % mileage bonus.