I'm a huge fan of Omega's...the equal of any Swiss watches, are super rugged and not overpriced like a Rolex (and I like Rolex; I'll probably get a Sea Dweller one day, but I know the brand is about 70% hype). I have an Omega X-33 and like it a lot; it has the functions that I need (4 timezones are easily displayed, though I really just use it for Zulu, homeplate and where ever I'm hanging my hat), it has an 82 decibel alarm, and a handy backlight to use in the plane. It has everything you need and having an engraved caseback is a cool memento of your time flying.
That being said, you have two great choices. The Speedmaster Professional is the iconic Moonwatch, worn by countless steely-eyed astronauts and still the only watch approved by NASA for EVA. When I think of a chronograph (a watch with a stopwatch function...on that watch the seconds hand is in the register at 9 o'clock), that is the watch I think of.
Plusses? It is easily read in low light, it keeps near COSC specs in its time keeping, and it is celebrating its 50 year anniversary this year. The minuses? The crystal is Hesalite (a type of plastic) and scratches (this can be buffed out by products like Polywatch...google it), you have to manually wind it, low water resistance (careful swimming, and no diving)and it has no date function. Because of this I wouldn't want it as a primary watch. Still, it is a great watch with a storied history.
Your Seamaster GMT is a great watch, especially with the GMT function (that is, the red hand on it will point to a second timezone and make a revolution around the clockface once every 24 hours). It is very similar to the watches worn by James Bond in the movies since Goldeneye, with some changes to it. Different movement, applied indeces, GMT function. Because of these changes it is very expensive; the Co-axial movement (a relatively new movement, proprietary to Omega that is supposed to improve accuracy and length of time between servicing) usually boosts the price of the watch 1000 bucks. If dad doesn't mind, go for it; still it is pricey when you could probably find the watch it was originally based on (the 2531.80.00, w/out GMT function) for a lot less, as they were discontinued this year, but a lot of dealers still have them. Or you could get the 2220.80.00 (it is the watch used in the current Bond film; an update of the 2531.80.00) and save some dough as well, though it does have the co-axial movement like the GMT.
Plusses: Scratch-proof sapphire crystal, great water resistance (you could dive with it), the movement is one of the most significant horological advances in the last 50 years, and the second timezone is helpful to pilots. Minuses: Movement is more expensive than comparable watches, it doesn't have the GMT markers on the bezel, i.e., you couldn't move the bezel and track a third timezone.
I would probably get the Seamaster of your two choices; better water resistance, scratch resistance, and the date feature make it more versatile.