My Aquaclears won't reprime if the water level drops more than 3 or 4 inches... in other words, every time I do a partial water change. Maybe acceptable for some, but not for me...
As for Emperors clogging on one side only, I've never seen this, in part, because there is no reason the mechanical media on one side would clog before that on the other. Also, Emperors have a spraybar that feeds the biowheel independent of water passing thru the mechanical media. I don't think it's possible that clogged mechanical media would interfere with the biowheel. Maybe on a Penguin, which has not spraybar, but not on an Emperor. I could be mistaken, but I have a number of Emps and have never, ever seen this problem. (Of course, I try to avoid letting my filters run until the media clogs.)
I think statements like 'x filter is too small for a xx gallon tank' are misleading, because stocking levels and maintenance are as important as filter throughput. An Emp 400 could be more than enough on a moderately stocked 60g. It would be insufficient for a tank of that size, though, stocked heavily or with messy fish (e.g., cichlids).
I still think two filters are safer than one big one. Each to his (or her) own, though...
Jim