It's like asking whether you should buy a Mustang or Camaro.
It basically comes down to what characteristics you value more:
1)Looks: MGA is gorgeous, sexy, sleek. TR3 is aggressive, somewhat dumpy to some, but unmistakable. TR3 stands out more, and is more popular with guys. Women like the lines of MGA.
2)Power: MGA is nearly 40hp down on a TR3. TR3 is torquey, and if you think you can only get axle hop in a muscle car, you've never dumped the clutch on a TR3! (I once had my throttle linkage pop-off due to the shake from a drop-clutch full-throttle launch.)
3)Handling: MGA is smooth and graceful, and more compliant -- one of the best of the era. TR3: quick steering but understeer in the dry and oversteer in the wet. If you can four wheel drift a stock TR3 on dry pavement, you can get work as a stunt driver in Hollywood! That being said the TR3 is FUN to throw around.
Tranny: The only tranny that's more fun to shift than a TR3 is a Miata. Stubby little lever is great - and the 3-4 transition just feels great! Not that the MGA is bad. Just not as magical in my opinion.
Value: Now about the same
Rarity: You see more TR3s around. Neither is rare, but you generally will see 3-to-1 TR3:MGA.
Comfort: About the same, provided you're under 6 feet. Over 6 feet, and you'll want a TR3, which can fit guys up 7 feet in pre-TS60,000 cars without a package shelf to block the seatback.
Bottom Line: The old collectors' line used to be "MGAs cost half as much as TR3s because they're half the car," but it is no longer true.
It comes down to which car you think looks better and feels better with you in the driver's seat. I personally love to be able to scrape my knuckles on the ground while holding the steering wheel. The sense of speed with those cut-down doors in a TR3 is hard to beat.
But I'd buy a MGA in heartbeat if I could justify it to the wife!