Alan,
As you know, Thompson's "Big Five" -- Jasper, Banff, St. George's, Capilano and Highlands Links -- ALL feature five par-3s. Interesting fact, isn't it.
Re the one-shot holes at Jasper and Banff, I'll say both sets of par-3s are very typical of Thompson's best work, specifically with regard to variety. Overall, it's a tough comparison; difficult to say which collection is better.
Let's try a Ran Morrissett match-play scenario, to see (using Banff's current sequence):
#4 Jasper vs. #2 Banff
ALL SQUARE (Both very good holes)
#7 Jasper vs. #4 Banff
BANFF 1UP (Devil's Cauldron wins)
#9 Jasper vs. #8 Banff
ALL SQUARE (Quirky Cleopatra wins)
#12 Jasper vs. #10 Banff
BANFF 1UP (Banff's 10th is an excellent hole, played over a corner of the Bow River)
#15 Jasper vs. #13 Banff
ALL SQUARE (The short 15th, Bad Baby, ties it up in the end... Canada's "2 or 20" hole!)
There you go! For whatever it's worth 
Frankly, all 10 holes noted above are very, very good.
Having played both this week, I thought I'd weigh in here...
#4 Jasper vs. #2 Banff
- A difficult choice since the long par-3 is so rarely well done, and this brute is both visually attractive with its green set into the hillside on the left, but also really offering the golfer the choice of playing short of the green to a wide fairway, or risk reaching the green which is narrowed at the front by flanking bunkers. But I think Banff #2 is the better hole. The dip in the fairway and bunkering short of the green help to hide the elevation change, though the fact that the golfer cannot see much of the putting surface should help to give an idea that the hole plays uphill. It's impossible to see from the tee, but the angled green is massive, some forty yards deep and sharply tilted from right to left. Golfers are encourage to play boldly as bailing out left leaves a very speedy recovery.
Banff 1UP
#7 Jasper vs. #4 Banff
Not a particularly difficult choice, comparing the spectacularly sited Devil's Cauldron with the somewhat mundane 7th at Jasper. Not that 7 at Jasper is an easy hole, far from it, which is almost surprising given how simple it looks. The steep false-front means a running approach is out of the question and the back-to-front tilted green will receive approaches, but heaven help the golfer that carries his tee shot too far and finds the rear bunker.
Banff 2UP
#9 Jasper vs. #8 Banff
I was reminded of Ross' 4th at Bedford Springs when I played Jasper's 9th. Now, Jasper's hole is eminently more playable, even allowing for a well thought-out running approach, but it's a hole that took some serious balls to build. At over 230 yards, few golfers will find the putting surface and rather than having soft features on a hole where most will miss, Thompson showed no mercy challenging the golfer with cross-bunkering, deep fronting green-side bunkers, and sharp fall-offs left, long and right, the latter two into flat-bottomed bunkers. Truly a unique and amazing hole.
Banff 1UP
#12 Jasper vs. #10 Banff
Not a difficult decision with Banff's 10th playing across the edge of the Bow River and Jasper's 12th being among the course's most forgettable holes. The angled green adds to the interest as bailing out away from the river leaves a challenging recovery to a green that runs away.
Banff 2UP
#15 Jasper vs. #13 Banff
It is amazing that a hole that looks so inviting from the tee can be among the most frightening short par-3s I've ever played. Especially without wind the 15th at Jasper at 130 yards should be a birdie hole, but golfers steering away from trouble (which is short, left, right and long!) may find themselves making some poor swings.
Banff 1UP