Well, having shot and loaded for both for over 50 yrs now, I'd say that if limited to store bought ammunition, I'd go with a .45 Colt...plenty of power in those old pointy slugs, some would say enough for any legit purpose in the lower 48...two legged or four, it has the mustard to do the job. There are good guns made for it too. Ones from Ruger, Colt SAA's, and S&W plus a bunch of wannabees. Cylinder throats may be a touch small in Rugers giving less than stellar accuracy with lead alloy bullets, but are easily remedied with a bit of reaming, my New Vaquero did at least...but a lll generation Colt SAA with a 7-1/2" bbl. was just right...both at .453"
But...the .44 Special too, is fine cartridge...better in handloads with a modest increase over SAAMI specs. Ruger makes outstanding single actions for it, as does Colt and S&W. But factory ammunition is anemic at best and expensive when you find it. Brass is easily available and there is a wide variety of bullet shapes and weights to please any aficionado. The Special's smaller case volume lends itself better to smokeless powder...most any pistol or shotgun powder will do BTW and will turn in excellent results. Target loads at 700 fps with Bullseye or 231, or barn burners at 1200 fps are easily turned out and accuracy is universally superb. In my experience I've never found nor heard of a Ruger, Colt or S&W .44 Special that wouldn't shoot extremely well. My day in, day out load mimics Skelton's offering: 7.5 gr of Unique backing any good 240 gr LSWC for 950 fps from a ~4-1/2" bbl. I use it in a quartet of Ruger's, my #1 son's Colt SAA, a S&W M-24, and a half dozen .44 Magnums...it's that good.
So you pays your money and takes your pick, but given the choice and allowing for reloading, mine would be a .44 Special. Developing an outstanding load from 700-1200 fps is easy. Not so much with a .45 Colt. My guess is that big .45 case (designed for black powder) just has too much volume to burn smokeless well...and mismatched bore and cylinder throat dimensions are more prevalent.
Rclark gets my vote as our resident guru on all things .45 Coltish & is a great source of info, but may differ on some of the above...and while his advice is rock solid...I'll still take the Special. All of that notwithstanding, none other than Elmer Keith once said that were he confined solely to factory loads, he would pick a .45 Colt and not feel under-gunned for any legit purpose.
Here's my choice Best Regards, Rod